Bulk RNA-Seq: Data Pre-processing for June 22 Plexwell

Neil Zhao1, Anagha Tapaswi1 and Justin Colacino1

1Department of Environmental Health Sciences, School of Public Health, University of Michigan-Ann Arbor, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, USA

Abstract

In this brief workflow, we start with aligned featureCounts mapped at the gene-level and perform data pre-processing and exploratory analyses. Base R and the edgeR package are used to import, filter, and organize the raw counts data. We then finish off with data reduction visualizations and quality control checks. By doing so, this allows for ease in performing downstream differential expression analysis and gene set testing.

This pipeline is inspired by Law et al. 2018 and Justin Colacino’s ‘Komen plexwell processing.R’ script (unpublished).

Package

BiocStyle 2.25.1

1 Getting started

Data files and repositories

The raw counts and sample metadata data files are available from:

https://drive.google.com/drive/folders/1G2xSZfloEjk_cMuFKbglx8UmO7hVylcE

⊕Tip: Set your working directory by entering Ctrl + Shift + H You should download the files listed below and place them into a folder in your working directory.

Komen_Jun22_seqwell_counts.txt
Seq_well_re_runs_June2022.xlsx

Bioconductor/R Packages

Packages used:

• edgeR
• AnnotationDbi
• org.Hs.eg.db (Use for human gene annotations)
• org.Mm.eg.db (Use for mouse gene annotations)
• Biostrings
• tidyverse
• reshape2
• gplots
• glimma

To install the packages, you can:

• Install the latest releases individually through R. This version of the tutorial uses R version 4.2.0.
• Get the latest version of Bioconductor and packages by starting R and entering these commands:

if (!requireNamespace("BiocManager"))
    install.packages("BiocManager")
BiocManager::install(c("edgeR", "AnnotationDbi", 
                       "org.Hs.eg.db", "org.Mm.eg.db", "Biostrings", "tidyverse", "gplots", "Glimma"))

First, let’s load all the packages we will use to process and analyze the data.

2 Data packaging

The data for this pipeline comes from the June 22 Plexwell RNA-seqwell experiment. It includes the processed data (counts) for the 5-3-22 Komen experiment re-runs and extra experimental sample wells for Rachel Morgan, Katelyn Polemi, Linda Samuelson.

For reference, we re-processed the following samples for the Komen Plexwell Experiment on 5-3-2022:

Show/Hide

Table 1: Sample Re-runs for Komen Plexwell Experiment on 5/3/22
The Komen Plexwell re-runs includes n = 104/576 of the original experimental samples that had less than a <5E06 library size, or the total number of sequenced reads across all mapped genes in a sample run.

Pool Name	Sample	sample.id	Treatment	Description	Dose	lib.size
KCR 7518	KCR7518	CCATACTC.AGTTTCCT	BPA	Bisphenol A_1	0.1	4438319
KCR 7518	KCR7518	TCCTTGGC.AGTTTCCT	BPA	Bisphenol A_2	0.1	4592853
KCR 7518	KCR7518	TCACTCAC.AGTTTCCT	BPA	Bisphenol A_3	0.1	4830331
KCR 7518	KCR7518	CAGGCTTC.AGTTTCCT	BPA	Bisphenol A_4	1	4988069
KCR 7518	KCR7518	CCTACACA.AGTTTCCT	BPA	Bisphenol A_5	1	3906282
KCR 7518	KCR7518	ATGGAACA.AGTTTCCT	BPS	Bisphenol S_8	10	3986349
KCR 7889	KCR7889	CCATACTC.CCTCCATA	BPA	Bisphenol A_1	0.1	330286
KCR 7889	KCR7889	TCCTTGGC.CCTCCATA	BPA	Bisphenol A_2	0.1	700937
KCR 7889	KCR7889	TCACTCAC.CCTCCATA	BPA	Bisphenol A_3	0.1	664177
KCR 7889	KCR7889	CAGGCTTC.CCTCCATA	BPA	Bisphenol A_4	1	602852
KCR 7889	KCR7889	CCTACACA.CCTCCATA	BPA	Bisphenol A_5	1	590262
KCR 7889	KCR7889	CGCGTGAT.CCTCCATA	BPA	Bisphenol A_6	1	223327
KCR 7889	KCR7889	CATCTTCT.CCTCCATA	BPA	Bisphenol A_7	10	113064
KCR 7889	KCR7889	ACATCCTT.CCTCCATA	BPA	Bisphenol A_8	10	145697
KCR 7889	KCR7889	ACACAACA.CCTCCATA	BPA	Bisphenol A_9	10	463697
KCR 7889	KCR7889	TTGGCTGC.CCTCCATA	BPS	Bisphenol S_1	0.1	4643601
KCR 7889	KCR7889	ATGACACC.CCTCCATA	BPS	Bisphenol S_3	0.1	3850642
KCR 7889	KCR7889	TGTTGCAC.CCTCCATA	BPS	Bisphenol S_4	1	1067957
KCR 7889	KCR7889	ATTCTCCA.CCTCCATA	BPS	Bisphenol S_5	1	2892147
KCR 7889	KCR7889	CGCAACAG.CCTCCATA	BPS	Bisphenol S_6	1	1833794
KCR 7889	KCR7889	CTTCTGGC.CCTCCATA	BPS	Bisphenol S_7	10	522111
KCR 7889	KCR7889	ATGGAACA.CCTCCATA	BPS	Bisphenol S_8	10	571686
KCR 7889	KCR7889	CTAACAAC.CCTCCATA	BPS	Bisphenol S_9	10	1475635
KCR 7889	KCR7889	CAGGCCAT.CCTCCATA	PFNA	PFNA_1	0.1	337540
KCR 7889	KCR7889	CAACTCCG.CCTCCATA	PFNA	PFNA_2	0.1	518427
KCR 7889	KCR7889	ACCGACCA.CCTCCATA	PFNA	PFNA_3	0.1	81384
KCR 7889	KCR7889	GTGCGAGT.CCTCCATA	PFNA	PFNA_4	1	489221
KCR 7889	KCR7889	ATGCCGCT.CCTCCATA	PFNA	PFNA_5	1	519967
KCR 7889	KCR7889	TCCTCAGA.CCTCCATA	PFNA	PFNA_6	1	126051
KCR 7889	KCR7889	ACGCTGCA.CCTCCATA	PFNA	PFNA_7	10	101283
KCR 7889	KCR7889	CGATGGCA.CCTCCATA	PFNA	PFNA_8	10	98809
KCR 7889	KCR7889	CAACCGTG.CCTCCATA	PFNA	PFNA_9	10	281834
KCR 7953	KCR7953	CGCTCTTG.TATTTGAG	DMSO	Control 71	0	4005522
KCR 7953	KCR7953	TGAACTCT.TATTTGAG	DMSO	Control 72	0	556342
KCR 7953	KCR7953	ACTCACCG.TATTTGAG	Water	Control 61	0	2935786
KCR 7953	KCR7953	CCTTATGT.TATTTGAG	Water	Control 62	0	889909
KCR 7953	KCR7953	CCATACTC.TATTTGAG	BPA	Bisphenol A_1	0.1	4322
KCR 7953	KCR7953	TCCTTGGC.TATTTGAG	BPA	Bisphenol A_2	0.1	2670
KCR 7953	KCR7953	TCACTCAC.TATTTGAG	BPA	Bisphenol A_3	0.1	34642
KCR 7953	KCR7953	CAGGCTTC.TATTTGAG	BPA	Bisphenol A_4	1	2731
KCR 7953	KCR7953	CCTACACA.TATTTGAG	BPA	Bisphenol A_5	1	37554
KCR 7953	KCR7953	CGCGTGAT.TATTTGAG	BPA	Bisphenol A_6	1	30332
KCR 7953	KCR7953	CATCTTCT.TATTTGAG	BPA	Bisphenol A_7	10	4479
KCR 7953	KCR7953	ACATCCTT.TATTTGAG	BPA	Bisphenol A_8	10	1764
KCR 7953	KCR7953	ACACAACA.TATTTGAG	BPA	Bisphenol A_9	10	98017
KCR 7953	KCR7953	TTGGCTGC.TATTTGAG	BPS	Bisphenol S_1	0.1	328345
KCR 7953	KCR7953	GATGAGAA.TATTTGAG	BPS	Bisphenol S_2	0.1	165583
KCR 7953	KCR7953	ATGACACC.TATTTGAG	BPS	Bisphenol S_3	0.1	119687
KCR 7953	KCR7953	TGTTGCAC.TATTTGAG	BPS	Bisphenol S_4	1	14059
KCR 7953	KCR7953	ATTCTCCA.TATTTGAG	BPS	Bisphenol S_5	1	312456
KCR 7953	KCR7953	CGCAACAG.TATTTGAG	BPS	Bisphenol S_6	1	35607
KCR 7953	KCR7953	CTTCTGGC.TATTTGAG	BPS	Bisphenol S_7	10	15369
KCR 7953	KCR7953	ATGGAACA.TATTTGAG	BPS	Bisphenol S_8	10	2159
KCR 7953	KCR7953	CTAACAAC.TATTTGAG	BPS	Bisphenol S_9	10	57722
KCR 7953	KCR7953	TGGTGGAA.TATTTGAG	Cadmium_Chloride	Cadmium_Chloride_1	0.1	4142100
KCR 7953	KCR7953	CTGTACGC.TATTTGAG	Cadmium_Chloride	Cadmium_Chloride_2	0.1	2517570
KCR 7953	KCR7953	ACTCGAAT.TATTTGAG	Cadmium_Chloride	Cadmium_Chloride_7	10	854141
KCR 7953	KCR7953	ACGAAGCG.TATTTGAG	DDE	DDE_1	0.1	1569364
KCR 7953	KCR7953	CTCTCAGG.TATTTGAG	DDE	DDE_2	0.1	310580
KCR 7953	KCR7953	CACCGCAA.TATTTGAG	DDE	DDE_3	0.1	1159972
KCR 7953	KCR7953	TGCTCCGT.TATTTGAG	DDE	DDE_4	1	401552
KCR 7953	KCR7953	CGAGCATT.TATTTGAG	DDE	DDE_5	1	70195
KCR 7953	KCR7953	ACCGTTCC.TATTTGAG	DDE	DDE_6	1	1311310
KCR 7953	KCR7953	TCAAGGAT.TATTTGAG	DDE	DDE_7	10	615546
KCR 7953	KCR7953	CAAGTGAC.TATTTGAG	DDE	DDE_8	10	444754
KCR 7953	KCR7953	CAGAGTGG.TATTTGAG	DDE	DDE_9	10	72186
KCR 7953	KCR7953	CAGGCCAT.TATTTGAG	PFNA	PFNA_1	0.1	6665
KCR 7953	KCR7953	CAACTCCG.TATTTGAG	PFNA	PFNA_2	0.1	3072
KCR 7953	KCR7953	ACCGACCA.TATTTGAG	PFNA	PFNA_3	0.1	61567
KCR 7953	KCR7953	GTGCGAGT.TATTTGAG	PFNA	PFNA_4	1	32518
KCR 7953	KCR7953	ATGCCGCT.TATTTGAG	PFNA	PFNA_5	1	52864
KCR 7953	KCR7953	TCCTCAGA.TATTTGAG	PFNA	PFNA_6	1	13358
KCR 7953	KCR7953	ACGCTGCA.TATTTGAG	PFNA	PFNA_7	10	25890
KCR 7953	KCR7953	CGATGGCA.TATTTGAG	PFNA	PFNA_8	10	1355
KCR 7953	KCR7953	CAACCGTG.TATTTGAG	PFNA	PFNA_9	10	2671
KCR 8195	KCR8195	CCACAATG.TCATATAT	Sodium_Arsenite	Sodium_Arsenite_7	10	4404878
KCR 8195	KCR8195	TACAGAGT.TCATATAT	Sodium_Arsenite	Sodium_Arsenite_9	10	2395550
KCR 8519	KCR8519	TACAGAGT.ATGTATCA	Sodium_Arsenite	Sodium_Arsenite_9	10	4458760
KCR 8580	KCR8580	CCATACTC.CAATGCAA	BPA	Bisphenol A_1	0.1	190179
KCR 8580	KCR8580	TCCTTGGC.CAATGCAA	BPA	Bisphenol A_2	0.1	402214
KCR 8580	KCR8580	TCACTCAC.CAATGCAA	BPA	Bisphenol A_3	0.1	366393
KCR 8580	KCR8580	CAGGCTTC.CAATGCAA	BPA	Bisphenol A_4	1	286710
KCR 8580	KCR8580	CCTACACA.CAATGCAA	BPA	Bisphenol A_5	1	204553
KCR 8580	KCR8580	CGCGTGAT.CAATGCAA	BPA	Bisphenol A_6	1	238993
KCR 8580	KCR8580	CATCTTCT.CAATGCAA	BPA	Bisphenol A_7	10	569666
KCR 8580	KCR8580	ACATCCTT.CAATGCAA	BPA	Bisphenol A_8	10	122211
KCR 8580	KCR8580	ACACAACA.CAATGCAA	BPA	Bisphenol A_9	10	110789
KCR 8580	KCR8580	ATGACACC.CAATGCAA	BPS	Bisphenol S_3	0.1	3715079
KCR 8580	KCR8580	TGTTGCAC.CAATGCAA	BPS	Bisphenol S_4	1	3866428
KCR 8580	KCR8580	ATTCTCCA.CAATGCAA	BPS	Bisphenol S_5	1	2662372
KCR 8580	KCR8580	CGCAACAG.CAATGCAA	BPS	Bisphenol S_6	1	2456087
KCR 8580	KCR8580	CTTCTGGC.CAATGCAA	BPS	Bisphenol S_7	10	501850
KCR 8580	KCR8580	ATGGAACA.CAATGCAA	BPS	Bisphenol S_8	10	433595
KCR 8580	KCR8580	CTAACAAC.CAATGCAA	BPS	Bisphenol S_9	10	412276
KCR 8580	KCR8580	CAGAGTGG.CAATGCAA	DDE	DDE_9	10	4263103
KCR 8580	KCR8580	CAGGCCAT.CAATGCAA	PFNA	PFNA_1	0.1	330140
KCR 8580	KCR8580	CAACTCCG.CAATGCAA	PFNA	PFNA_2	0.1	274683
KCR 8580	KCR8580	ACCGACCA.CAATGCAA	PFNA	PFNA_3	0.1	160945
KCR 8580	KCR8580	GTGCGAGT.CAATGCAA	PFNA	PFNA_4	1	232231
KCR 8580	KCR8580	ATGCCGCT.CAATGCAA	PFNA	PFNA_5	1	228138
KCR 8580	KCR8580	TCCTCAGA.CAATGCAA	PFNA	PFNA_6	1	63019
KCR 8580	KCR8580	ACGCTGCA.CAATGCAA	PFNA	PFNA_7	10	57682
KCR 8580	KCR8580	CGATGGCA.CAATGCAA	PFNA	PFNA_8	10	49925
KCR 8580	KCR8580	CAACCGTG.CAATGCAA	PFNA	PFNA_9	10	133796

2.1 Reading in the data

⊕*NOTE: When publishing your rmarkdown file, these files will be deleted from the folder due to the knitr embedding and pandoc file conversion process. To prevent this, go to the folder where you saved these file(s), right click the file -> ‘properties’ -> select the ‘Read-only’ checkbox -> hit ‘apply’ -> exit by clicking ‘OK’. To get started, set up an RStudio project folder (i.e. ~/data directory/) specifying where you have saved the data files. Import and read in the counts and sample metadata from above.*

# Read the raw counts data into R
seqdata <- read.table("~/Komen_Jun22_seqwell_counts.txt", header = T)

# Read the sample metadata information into R
all.metadata <- readxl::read_xlsx("~/Seq_well_re_runs_June2022.xlsx")

The seqdata file contains the gene-level raw counts for a given sample. Let’s take a quick glance at the data. You can use the dim command to see how many rows and columns the data frame has. The colnames command will tell you the names of the columns. Use the head or tail command to see a preview of the first or last 6 lines of the data frame, respectively.

dim(seqdata)

## [1] 95566   198

head(seqdata)

## # A tibble: 6 × 198
##   Geneid Chr   Start End   Strand Length X.nfs…¹ X.nfs…² X.nfs…³ X.nfs…⁴ X.nfs…⁵
##   <chr>  <chr> <chr> <chr> <chr>   <int>   <int>   <int>   <int>   <int>   <int>
## 1 DDX11… HUMA… 1186… 1222… +;+;+…   1756       0       0       0       0       0
## 2 WASH7P HUMA… 1436… 1482… -;-;-…   2073       0     154     303     225     487
## 3 MIR13… HUMA… 2955… 3003… +;+;+…   1021       0       0       0       0       0
## 4 FAM13… HUMA… 3455… 3517… -;-;-…   1219       0       0       0       0       0
## 5 OR4G4P HUMA… 5247… 5331… +;+;+     947       0       0       0       0       0
## 6 OR4G1… HUMA… 62948 63887 +         940       0       0       0       0       0
## # … with 187 more variables:
## #   X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_TCAAGGAT.TCATATAT_S538Aligned.sortedByCoord.out.bam <int>,
## #   X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_GTGCGTTC.ATGTATCA_S483Aligned.sortedByCoord.out.bam <int>,
## #   X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CCACAATG.TCATATAT_S514Aligned.sortedByCoord.out.bam <int>,
## #   X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_GTGCGTTC.TCATATAT_S579Aligned.sortedByCoord.out.bam <int>,
## #   X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CTGGTCGT.TCATATAT_S519Aligned.sortedByCoord.out.bam <int>,
## #   X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_ACCGTTCC.ATGTATCA_S441Aligned.sortedByCoord.out.bam <int>, …
## # ℹ Use `colnames()` to see all variable names

colnames(seqdata)

##   [1] "Geneid"                                                                                                                                
##   [2] "Chr"                                                                                                                                   
##   [3] "Start"                                                                                                                                 
##   [4] "End"                                                                                                                                   
##   [5] "Strand"                                                                                                                                
##   [6] "Length"                                                                                                                                
##   [7] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_GTTATCGA.TCATATAT_S574Aligned.sortedByCoord.out.bam"
##   [8] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_TTCCATTC.ATGTATCA_S476Aligned.sortedByCoord.out.bam"
##   [9] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CTCTCAGG.ATGTATCA_S437Aligned.sortedByCoord.out.bam"
##  [10] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_TACAGAGT.ATGTATCA_S420Aligned.sortedByCoord.out.bam"
##  [11] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_TGCTCCGT.ATGTATCA_S439Aligned.sortedByCoord.out.bam"
##  [12] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_TCAAGGAT.TCATATAT_S538Aligned.sortedByCoord.out.bam"
##  [13] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_GTGCGTTC.ATGTATCA_S483Aligned.sortedByCoord.out.bam"
##  [14] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CCACAATG.TCATATAT_S514Aligned.sortedByCoord.out.bam"
##  [15] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_GTGCGTTC.TCATATAT_S579Aligned.sortedByCoord.out.bam"
##  [16] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CTGGTCGT.TCATATAT_S519Aligned.sortedByCoord.out.bam"
##  [17] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_ACCGTTCC.ATGTATCA_S441Aligned.sortedByCoord.out.bam"
##  [18] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_ACACAACA.ATGTATCA_S462Aligned.sortedByCoord.out.bam"
##  [19] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CGCGTGAT.ATGTATCA_S459Aligned.sortedByCoord.out.bam"
##  [20] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_ATGACACC.TCATATAT_S543Aligned.sortedByCoord.out.bam"
##  [21] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_TCCTATCT.TCATATAT_S511Aligned.sortedByCoord.out.bam"
##  [22] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_AACCAATC.TCATATAT_S505Aligned.sortedByCoord.out.bam"
##  [23] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_GCCAGTGT.ATGTATCA_S482Aligned.sortedByCoord.out.bam"
##  [24] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_TCTATTGG.TCATATAT_S506Aligned.sortedByCoord.out.bam"
##  [25] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CATCTTCT.TCATATAT_S556Aligned.sortedByCoord.out.bam"
##  [26] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CCGAGTTA.ATGTATCA_S393Aligned.sortedByCoord.out.bam"
##  [27] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_TTCACACT.ATGTATCA_S413Aligned.sortedByCoord.out.bam"
##  [28] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CTAGCCGA.TCATATAT_S571Aligned.sortedByCoord.out.bam"
##  [29] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CGCTCTTG.ATGTATCA_S434Aligned.sortedByCoord.out.bam"
##  [30] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_ACTCACCG.ATGTATCA_S388Aligned.sortedByCoord.out.bam"
##  [31] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_ATGCCGCT.TCATATAT_S563Aligned.sortedByCoord.out.bam"
##  [32] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_TGGTACAG.TCATATAT_S527Aligned.sortedByCoord.out.bam"
##  [33] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CCTGTTAC.ATGTATCA_S403Aligned.sortedByCoord.out.bam"
##  [34] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CGCAACAG.ATGTATCA_S450Aligned.sortedByCoord.out.bam"
##  [35] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CTAGCCGA.ATGTATCA_S475Aligned.sortedByCoord.out.bam"
##  [36] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_ACTCGAAT.ATGTATCA_S400Aligned.sortedByCoord.out.bam"
##  [37] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CGCGTGAT.TCATATAT_S555Aligned.sortedByCoord.out.bam"
##  [38] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_AAGTACCT.TCATATAT_S502Aligned.sortedByCoord.out.bam"
##  [39] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_GATGAGAA.ATGTATCA_S446Aligned.sortedByCoord.out.bam"
##  [40] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CCTACACA.ATGTATCA_S458Aligned.sortedByCoord.out.bam"
##  [41] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_TCCTTGGC.TCATATAT_S551Aligned.sortedByCoord.out.bam"
##  [42] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_ACCTGAGC.TCATATAT_S523Aligned.sortedByCoord.out.bam"
##  [43] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_GATGAGAA.TCATATAT_S542Aligned.sortedByCoord.out.bam"
##  [44] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_AACGCTTG.TCATATAT_S528Aligned.sortedByCoord.out.bam"
##  [45] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_TGGACAAC.TCATATAT_S575Aligned.sortedByCoord.out.bam"
##  [46] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CATCTTCT.ATGTATCA_S460Aligned.sortedByCoord.out.bam"
##  [47] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_ATTCGCAG.TCATATAT_S522Aligned.sortedByCoord.out.bam"
##  [48] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_GGTGTGAC.TCATATAT_S513Aligned.sortedByCoord.out.bam"
##  [49] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CGTAATTC.TCATATAT_S521Aligned.sortedByCoord.out.bam"
##  [50] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_ACATCCTT.ATGTATCA_S461Aligned.sortedByCoord.out.bam"
##  [51] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CGATGGCA.ATGTATCA_S470Aligned.sortedByCoord.out.bam"
##  [52] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CCAGGTAA.ATGTATCA_S429Aligned.sortedByCoord.out.bam"
##  [53] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_ACTCGAAT.TCATATAT_S496Aligned.sortedByCoord.out.bam"
##  [54] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_TGGACAAC.ATGTATCA_S479Aligned.sortedByCoord.out.bam"
##  [55] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_GTTAAGCA.ATGTATCA_S408Aligned.sortedByCoord.out.bam"
##  [56] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CTGTACGC.TCATATAT_S491Aligned.sortedByCoord.out.bam"
##  [57] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CAGGCTTC.TCATATAT_S553Aligned.sortedByCoord.out.bam"
##  [58] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CTAACAAC.ATGTATCA_S453Aligned.sortedByCoord.out.bam"
##  [59] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_TCAACTGA.ATGTATCA_S472Aligned.sortedByCoord.out.bam"
##  [60] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_GTTCGTCT.TCATATAT_S524Aligned.sortedByCoord.out.bam"
##  [61] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CCTTATGT.TCATATAT_S485Aligned.sortedByCoord.out.bam"
##  [62] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CACCGCAA.TCATATAT_S534Aligned.sortedByCoord.out.bam"
##  [63] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CAACCGTG.TCATATAT_S567Aligned.sortedByCoord.out.bam"
##  [64] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_GTACCAGC.TCATATAT_S497Aligned.sortedByCoord.out.bam"
##  [65] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_ATTCCGTA.TCATATAT_S529Aligned.sortedByCoord.out.bam"
##  [66] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CCGAGTTA.TCATATAT_S489Aligned.sortedByCoord.out.bam"
##  [67] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CTATTCCA.TCATATAT_S576Aligned.sortedByCoord.out.bam"
##  [68] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CTCGTACA.ATGTATCA_S424Aligned.sortedByCoord.out.bam"
##  [69] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_TCCTCAGA.ATGTATCA_S468Aligned.sortedByCoord.out.bam"
##  [70] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CGAGCATT.TCATATAT_S536Aligned.sortedByCoord.out.bam"
##  [71] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CAGGAAGG.TCATATAT_S494Aligned.sortedByCoord.out.bam"
##  [72] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_TGAATGTG.TCATATAT_S507Aligned.sortedByCoord.out.bam"
##  [73] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_GGCTCCTA.ATGTATCA_S396Aligned.sortedByCoord.out.bam"
##  [74] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_ATGGAACA.TCATATAT_S548Aligned.sortedByCoord.out.bam"
##  [75] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_TCAGATAC.TCATATAT_S515Aligned.sortedByCoord.out.bam"
##  [76] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CCATACTC.ATGTATCA_S454Aligned.sortedByCoord.out.bam"
##  [77] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_GTTATCGA.ATGTATCA_S478Aligned.sortedByCoord.out.bam"
##  [78] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_TGAATGTG.ATGTATCA_S411Aligned.sortedByCoord.out.bam"
##  [79] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_AATGTGCC.ATGTATCA_S405Aligned.sortedByCoord.out.bam"
##  [80] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_TGTAAGAC.TCATATAT_S518Aligned.sortedByCoord.out.bam"
##  [81] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_GGAGCTAT.TCATATAT_S487Aligned.sortedByCoord.out.bam"
##  [82] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_TGGTGACT.ATGTATCA_S392Aligned.sortedByCoord.out.bam"
##  [83] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CGCTCTTG.TCATATAT_S530Aligned.sortedByCoord.out.bam"
##  [84] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CAAGTAGT.TCATATAT_S569Aligned.sortedByCoord.out.bam"
##  [85] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_TGAACTCT.ATGTATCA_S435Aligned.sortedByCoord.out.bam"
##  [86] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_AACGCTTG.ATGTATCA_S432Aligned.sortedByCoord.out.bam"
##  [87] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CACCGCAA.ATGTATCA_S438Aligned.sortedByCoord.out.bam"
##  [88] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_TGCTCCGT.TCATATAT_S535Aligned.sortedByCoord.out.bam"
##  [89] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_ATTCTCCA.TCATATAT_S545Aligned.sortedByCoord.out.bam"
##  [90] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_TTGGCTGC.ATGTATCA_S445Aligned.sortedByCoord.out.bam"
##  [91] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_ATGACACC.ATGTATCA_S447Aligned.sortedByCoord.out.bam"
##  [92] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_TCACTCAC.ATGTATCA_S456Aligned.sortedByCoord.out.bam"
##  [93] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_ATGGAACA.ATGTATCA_S452Aligned.sortedByCoord.out.bam"
##  [94] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_GTGCGAGT.ATGTATCA_S466Aligned.sortedByCoord.out.bam"
##  [95] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_TGTTGCAC.ATGTATCA_S448Aligned.sortedByCoord.out.bam"
##  [96] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_ACCGTTCC.TCATATAT_S537Aligned.sortedByCoord.out.bam"
##  [97] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CAAGTGAC.ATGTATCA_S443Aligned.sortedByCoord.out.bam"
##  [98] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_GTTGACAG.TCATATAT_S500Aligned.sortedByCoord.out.bam"
##  [99] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CACATGGT.TCATATAT_S512Aligned.sortedByCoord.out.bam"
## [100] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_ATGGTCCG.ATGTATCA_S414Aligned.sortedByCoord.out.bam"
## [101] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CTTGTTGG.ATGTATCA_S421Aligned.sortedByCoord.out.bam"
## [102] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_ACATCCTT.TCATATAT_S557Aligned.sortedByCoord.out.bam"
## [103] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_ACGAAGCG.TCATATAT_S532Aligned.sortedByCoord.out.bam"
## [104] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_ACACAACA.TCATATAT_S558Aligned.sortedByCoord.out.bam"
## [105] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CCATTGCG.TCATATAT_S508Aligned.sortedByCoord.out.bam"
## [106] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_ATAGATCC.ATGTATCA_S390Aligned.sortedByCoord.out.bam"
## [107] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_ATTCCGTA.ATGTATCA_S433Aligned.sortedByCoord.out.bam"
## [108] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CAGGCCAT.ATGTATCA_S463Aligned.sortedByCoord.out.bam"
## [109] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CTGCGAAC.ATGTATCA_S481Aligned.sortedByCoord.out.bam"
## [110] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CAGGCTTC.ATGTATCA_S457Aligned.sortedByCoord.out.bam"
## [111] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_ACCGACCA.TCATATAT_S561Aligned.sortedByCoord.out.bam"
## [112] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_TCAAGGAT.ATGTATCA_S442Aligned.sortedByCoord.out.bam"
## [113] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_TACAGAGT.TCATATAT_S516Aligned.sortedByCoord.out.bam"
## [114] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_ATGGTCCG.TCATATAT_S510Aligned.sortedByCoord.out.bam"
## [115] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_GTGTCCAT.TCATATAT_S570Aligned.sortedByCoord.out.bam"
## [116] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_TTGGCTGC.TCATATAT_S541Aligned.sortedByCoord.out.bam"
## [117] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CACAGTCT.ATGTATCA_S430Aligned.sortedByCoord.out.bam"
## [118] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CTGCGAAC.TCATATAT_S577Aligned.sortedByCoord.out.bam"
## [119] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_ACGCTGCA.ATGTATCA_S469Aligned.sortedByCoord.out.bam"
## [120] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CTAACAAC.TCATATAT_S549Aligned.sortedByCoord.out.bam"
## [121] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CGTAATTC.ATGTATCA_S425Aligned.sortedByCoord.out.bam"
## [122] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_TCTATTGG.ATGTATCA_S410Aligned.sortedByCoord.out.bam"
## [123] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_ACTCACCG.TCATATAT_S484Aligned.sortedByCoord.out.bam"
## [124] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_TCCTTGGC.ATGTATCA_S455Aligned.sortedByCoord.out.bam"
## [125] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_ACGAAGCG.ATGTATCA_S436Aligned.sortedByCoord.out.bam"
## [126] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CAGAGTGG.ATGTATCA_S444Aligned.sortedByCoord.out.bam"
## [127] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CAACTCCG.TCATATAT_S560Aligned.sortedByCoord.out.bam"
## [128] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_GTGCGAGT.TCATATAT_S562Aligned.sortedByCoord.out.bam"
## [129] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_ATGCCGCT.ATGTATCA_S467Aligned.sortedByCoord.out.bam"
## [130] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CAGGCCAT.TCATATAT_S559Aligned.sortedByCoord.out.bam"
## [131] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CTATTCCA.ATGTATCA_S480Aligned.sortedByCoord.out.bam"
## [132] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CAGAGTGG.TCATATAT_S540Aligned.sortedByCoord.out.bam"
## [133] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_TCACTCAC.TCATATAT_S552Aligned.sortedByCoord.out.bam"
## [134] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CTGTACGC.ATGTATCA_S395Aligned.sortedByCoord.out.bam"
## [135] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_GTTCGTCT.ATGTATCA_S428Aligned.sortedByCoord.out.bam"
## [136] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_TTCACACT.TCATATAT_S509Aligned.sortedByCoord.out.bam"
## [137] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CAGGAAGG.ATGTATCA_S398Aligned.sortedByCoord.out.bam"
## [138] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_GTTAAGCA.TCATATAT_S504Aligned.sortedByCoord.out.bam"
## [139] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_GGCTCCTA.TCATATAT_S492Aligned.sortedByCoord.out.bam"
## [140] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CCTACACA.TCATATAT_S554Aligned.sortedByCoord.out.bam"
## [141] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CGCAACAG.TCATATAT_S546Aligned.sortedByCoord.out.bam"
## [142] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CTCGTACA.TCATATAT_S520Aligned.sortedByCoord.out.bam"
## [143] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_ACTTCAAC.TCATATAT_S498Aligned.sortedByCoord.out.bam"
## [144] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_AATGTGCC.TCATATAT_S501Aligned.sortedByCoord.out.bam"
## [145] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_GGAGCTAT.ATGTATCA_S391Aligned.sortedByCoord.out.bam"
## [146] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CGACTAGC.ATGTATCA_S407Aligned.sortedByCoord.out.bam"
## [147] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_TCCTATCT.ATGTATCA_S415Aligned.sortedByCoord.out.bam"
## [148] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_TGGTACAG.ATGTATCA_S431Aligned.sortedByCoord.out.bam"
## [149] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_GTTGACAG.ATGTATCA_S404Aligned.sortedByCoord.out.bam"
## [150] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_TGTTGCAC.TCATATAT_S544Aligned.sortedByCoord.out.bam"
## [151] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CTTCTGGC.TCATATAT_S547Aligned.sortedByCoord.out.bam"
## [152] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CGACTAGC.TCATATAT_S503Aligned.sortedByCoord.out.bam"
## [153] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_GTACCAGC.ATGTATCA_S401Aligned.sortedByCoord.out.bam"
## [154] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CTAAGGCG.TCATATAT_S573Aligned.sortedByCoord.out.bam"
## [155] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CCATTGCG.ATGTATCA_S412Aligned.sortedByCoord.out.bam"
## [156] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_ACGCTGCA.TCATATAT_S565Aligned.sortedByCoord.out.bam"
## [157] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CACAGTCT.TCATATAT_S526Aligned.sortedByCoord.out.bam"
## [158] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CGTCTGAA.ATGTATCA_S399Aligned.sortedByCoord.out.bam"
## [159] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CGAGCATT.ATGTATCA_S440Aligned.sortedByCoord.out.bam"
## [160] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CCTGTTAC.TCATATAT_S499Aligned.sortedByCoord.out.bam"
## [161] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CCACAATG.ATGTATCA_S418Aligned.sortedByCoord.out.bam"
## [162] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CAAGTGAC.TCATATAT_S539Aligned.sortedByCoord.out.bam"
## [163] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_TTCCATTC.TCATATAT_S572Aligned.sortedByCoord.out.bam"
## [164] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_AAGTACCT.ATGTATCA_S406Aligned.sortedByCoord.out.bam"
## [165] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CCTTATGT.ATGTATCA_S389Aligned.sortedByCoord.out.bam"
## [166] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CAGAAGAA.ATGTATCA_S397Aligned.sortedByCoord.out.bam"
## [167] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CTTGTTGG.TCATATAT_S517Aligned.sortedByCoord.out.bam"
## [168] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CGTCTGAA.TCATATAT_S495Aligned.sortedByCoord.out.bam"
## [169] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_AACCAATC.ATGTATCA_S409Aligned.sortedByCoord.out.bam"
## [170] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_TGGTGGAA.ATGTATCA_S394Aligned.sortedByCoord.out.bam"
## [171] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CCATACTC.TCATATAT_S550Aligned.sortedByCoord.out.bam"
## [172] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CGATGGCA.TCATATAT_S566Aligned.sortedByCoord.out.bam"
## [173] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_ATTCTCCA.ATGTATCA_S449Aligned.sortedByCoord.out.bam"
## [174] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_ACTTCAAC.ATGTATCA_S402Aligned.sortedByCoord.out.bam"
## [175] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CACATGGT.ATGTATCA_S416Aligned.sortedByCoord.out.bam"
## [176] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_TCCTCAGA.TCATATAT_S564Aligned.sortedByCoord.out.bam"
## [177] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CAAGTAGT.ATGTATCA_S473Aligned.sortedByCoord.out.bam"
## [178] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CAGAAGAA.TCATATAT_S493Aligned.sortedByCoord.out.bam"
## [179] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CTTCTGGC.ATGTATCA_S451Aligned.sortedByCoord.out.bam"
## [180] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_GGTGTGAC.ATGTATCA_S417Aligned.sortedByCoord.out.bam"
## [181] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_TGAACTCT.TCATATAT_S531Aligned.sortedByCoord.out.bam"
## [182] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_TGGTGGAA.TCATATAT_S490Aligned.sortedByCoord.out.bam"
## [183] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CTCTCAGG.TCATATAT_S533Aligned.sortedByCoord.out.bam"
## [184] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_ATTCGCAG.ATGTATCA_S426Aligned.sortedByCoord.out.bam"
## [185] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_TGTAAGAC.ATGTATCA_S422Aligned.sortedByCoord.out.bam"
## [186] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_GTGTCCAT.ATGTATCA_S474Aligned.sortedByCoord.out.bam"
## [187] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CTAAGGCG.ATGTATCA_S477Aligned.sortedByCoord.out.bam"
## [188] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CAACTCCG.ATGTATCA_S464Aligned.sortedByCoord.out.bam"
## [189] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_GCCAGTGT.TCATATAT_S578Aligned.sortedByCoord.out.bam"
## [190] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_ACCTGAGC.ATGTATCA_S427Aligned.sortedByCoord.out.bam"
## [191] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_ACCGACCA.ATGTATCA_S465Aligned.sortedByCoord.out.bam"
## [192] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CAACCGTG.ATGTATCA_S471Aligned.sortedByCoord.out.bam"
## [193] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_TCAGATAC.ATGTATCA_S419Aligned.sortedByCoord.out.bam"
## [194] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_TCAACTGA.TCATATAT_S568Aligned.sortedByCoord.out.bam"
## [195] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_TGGTGACT.TCATATAT_S488Aligned.sortedByCoord.out.bam"
## [196] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_ATAGATCC.TCATATAT_S486Aligned.sortedByCoord.out.bam"
## [197] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_CCAGGTAA.TCATATAT_S525Aligned.sortedByCoord.out.bam"
## [198] "X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_CTGGTCGT.ATGTATCA_S423Aligned.sortedByCoord.out.bam"

The seqdata object also contains metadata information about the genes (one gene per row) in the wide-format:

• The first column contains the gene id symbols
• The second column has information about the genome alignment* ⊕*NOTE: The counts data was aligned to a combined human/mouse genome because of the Komen J2-fibroblast feeder layers and other experimental samples. When performing data packaging, make sure you’re working with the correct species for your gene annotations.
• The third, fourth, and fifth column(s) contain genomic location/mapping and strand orientation information
• The sixth column contains the gene lengths
• The remaining columns contain information about the number of mapped reads aligning to the genes in each experimental sample

The all.metadata file contains detailed information about our samples. We will need to use this to separate, annotate, and analyze our Plexwell samples by experiment later on.

metadata

2.2 Formating the data

As detailed by Phipson et al. (2020), we need to manipulate and reformat the seqdata raw counts table into a suitable format for downstream analysis. To do so, we will create a new counts matrix for each experiment. Using the first two columns in the seqdata dataframe, we can store the gene identifiers for a species (i.e. Geneid symbols) as the rownames and the sample ID information as the colnames . We will add additional annotation information about each gene later on as well.

Currently, the column names for the samples in the seqdata read counts table contain complex string identifiers. These are artefacts from the .fastq sequencing alignment and featureCounts post-alignment protocols.

X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_
X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_
Aligned.sortedByCoord.out.bam_[...]

Let’s parse these out for clarity before we create new count matrices. ⊕Tip: When data processing, it is recommended to limit the number of intermediary variables you generate in your Global Environment. For instance, use the magrittr pipe operator from dplyr (i.e. %>%) or the native R pipe operator (|> req. R 4.1+). This makes your code efficient and helps to prevent losing track of assigned variables.

# Clean up the counts table so we're only left with the 
# unique ID barcodes as the sample colnames and the Geneid symbols as the rownames
modified.counts <- seqdata %>% 
  `rownames<-`(.[,1]) %>% select(-Geneid) %>% #Remove the Geneid column once you've set the rownames
  select(starts_with('X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT') 
         & ends_with('Aligned.sortedByCoord.out.bam')) %>%
  rename_with(~str_remove
              (., 'X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.1_')) %>%
  rename_with(~str_remove
              (., 'X.nfs.colacino.Sequencing.ONES.Komen_Seqwell.6246.AT_nova.fastqs_6246.AT.6246.AT.2_')) %>% 
  rename_with(~str_remove(., 'Aligned.sortedByCoord.out.bam')) %>%
  rename_with(~str_remove(., '_S.*')) #remove parts of column name after certain characters

⊕Tip: When data processing, it is also recommended to perform various ‘sanity checks’. That is, confirm your results are what you expect. For instance, use the head or tail function to take a quick glance at your data.

#Look at the output 
modified.counts

2.3 Organizing sample information

Now that we’ve shortened the seqdata sample column names to contain only relevant information, we need to manipulate and match it with the all.metadata experimental design information. This will help to identify both the technical and biological replicates for a given experimental design factor.

Examples:

1. Komen Plexwell Re-run

• Group (i.e. ex-vivo patient derived cell-line)
• Treatment (i.e. chemicals, controls)
• Dose (i.e. 0, 0.1, 1, 10 uM)

2. Rachel Morgan’s Experiment

• organ (i.e. heart, brain, cortex)
• phenotype (i.e. sex, age, disease status/morbidity)

3. Katelyn Polemi’s Experiment

• cell types/models (i.e. MCF7, MCF10A)
• sample treatment (i.e. drug, control)
• treatment dose (i.e. 0.1, 1, 10 uM)

… and etc.

Let’s edit our all.metadata object to help separate the counts matrix based on experiment.

To match the all.metadata with the seqdata, we will use the i7 and i5 index barcode adapter sequences as our sample identifiers. Since the complementary DNA (cDNA) libraries for the RNA transcript pool were generated using reverse transcriptase, we need to make a new sample.ids column in the all.metadata for the seqdata colnames to match.

⊕Tip: When using the match function, the first argument is the order of the object we want (i.e. modified.counts) and the second argument is the object we wanted to be reordered (i.e. all.metadata). We directly subset these indices to reorder the rows of the all.metadata such that it matches the colnames of the modified.counts. Additionally, avoid manually parsing out the reverse transcripts; doing it by hand is error-prone and unnecessary.

# Reverse transcribe the i5 sequences into reverse complementary nucleotide sequences
all.metadata$`i5 Sequence` <- as.character(
  reverseComplement(DNAStringSet(all.metadata$`i5 Sequence`))
  )
  
# #Make a new sample.ids column in the metadata 
# which concatenates the i7 sequence + "." + reverse complementary i5 sequence
all.metadata <- all.metadata %>% 
  mutate(sample.id = paste0(.$`i7 Sequence*`, ".", .$`i5 Sequence`))

#Reorder the metadata rows so that it matches the order of the counts matrix columns
all.metadata <- all.metadata[match(colnames(modified.counts), all.metadata$sample.id), ]

Perform a sanity check and confirm the column names for modified.counts matches the sample.id column of the metadata and that the order is the same.

#Confirm the metadata and counts matrix match and are in the same order for the samples  
all(all.metadata$sample.id == colnames(modified.counts))

## [1] TRUE

2.4 Data splitting and exporting

Now that our counts and metadata files are formatted properly, we need to separate the sample counts based on experiment. To recap, we have counts datasets for four different RNA-seq experiments stored in the single modified.counts object:

1. Komen re-runs for the 5-3-22 experiment
2. Rachel Morgan
3. Katelyn Polemi
4. Linda Samuelson

We need to separate these experiments based on the following all.metadata patterns in the Description column:

1. Komen re-runs for the 5-3-22 experiment

• Contains “7518 | 7889 | 7953 | 8195 | 8519 | 8580”

2. Rachel Morgan

• Starts with “5Y | 6_”
• Contains “heart | brain | cortex”

3. Katelyn Polemi

• Contains “MCF7 | MCF10A”

4. Linda Samuelson

• Ends with “V1 | D1”

 

To split the counts data, we will need to first split the all.metadata. We can do this by using the base R grepL and tidyverse filter functions on the regex patterns listed above.

Essentially, we first place our desired pattern matches in a character vector using paste, where collapse denotes the logical operator for ‘or’ when indexing multiple patterns. The filter function then uses the logical outputs from grepl in the column we’re matching for and extracts the rows of matched data accordingly.

⊕Tip: Saving your results to a list is optional. However, it is good storage object housekeeping practice and helps with downstream processing.

#Split the all.metadata dataframe by filter & grep w/ multiple regex patterns
  split.metadata.list <- list(
    
    #Komen re-run samples
    filter(all.metadata, 
           grepl(paste(c("7518","7889", "7953","8195", "8519", "8580"), collapse = "|"),
                 all.metadata$Description)),
    
    #Rachel Morgan samples
    filter(all.metadata, 
           grepl(paste(c("heart","brain", "cortex","5Y", "6_"), collapse = "|"), 
                 all.metadata$Description)),
    
    #Katelyn Polemi samples
    filter(all.metadata,
           grepl(paste(c("MCF7","MCF10A"), collapse = "|"), 
                 all.metadata$Description)),
    
    #Linda Samuelson
    filter(all.metadata,
           grepl(paste(c("V1","D1"), collapse = "|"), all.metadata$Description))
    
      )
  
  #Be sure to name the metadata list entries in the proper order
  names(split.metadata.list) <- c("komenredo.metadata",
                                  "rachelm.metadata",
                                  "katelynp.metadata",
                                  "lindas.metadata")

Let’s check out the results:

split.metadata.list

## $komenredo.metadata
## # A tibble: 123 × 7
##    `Pool Name*`   `i7 Index Name*` i7 Sequence…¹ i5 In…² i5 Se…³ Descr…⁴ sampl…⁵
##    <chr>          <chr>            <chr>         <chr>   <chr>   <chr>   <chr>  
##  1 Library prep 1 A12              TTCCATTC      PB-L044 ATGTAT… 8580-P… TTCCAT…
##  2 Library prep 1 A05              TACAGAGT      PB-L044 ATGTAT… 7953-D… TACAGA…
##  3 Library prep 2 G07              TCAAGGAT      PB-L021 TCATAT… 8195-D… TCAAGG…
##  4 Library prep 2 G04              CCACAATG      PB-L021 TCATAT… 7889-B… CCACAA…
##  5 Library prep 2 D05              CTGGTCGT      PB-L021 TCATAT… 7889-B… CTGGTC…
##  6 Library prep 1 C10              ACACAACA      PB-L044 ATGTAT… 8580-B… ACACAA…
##  7 Library prep 1 H09              CGCGTGAT      PB-L044 ATGTAT… 8580-B… CGCGTG…
##  8 Library prep 2 D04              TCCTATCT      PB-L021 TCATAT… 7889-B… TCCTAT…
##  9 Library prep 2 F03              AACCAATC      PB-L021 TCATAT… 7889-B… AACCAA…
## 10 Library prep 2 G03              TCTATTGG      PB-L021 TCATAT… 7889-B… TCTATT…
## # … with 113 more rows, and abbreviated variable names ¹​`i7 Sequence*`,
## #   ²​`i5 Index Name`, ³​`i5 Sequence`, ⁴​Description, ⁵​sample.id
## # ℹ Use `print(n = ...)` to see more rows
## 
## $rachelm.metadata
## # A tibble: 32 × 7
##    `Pool Name*`   `i7 Index Name*` i7 Sequence…¹ i5 In…² i5 Se…³ Descr…⁴ sampl…⁵
##    <chr>          <chr>            <chr>         <chr>   <chr>   <chr>   <chr>  
##  1 Library prep 2 C12              GTTATCGA      PB-L021 TCATAT… 6_0.03… GTTATC…
##  2 Library prep 2 H12              GTGCGTTC      PB-L021 TCATAT… 6_Cont… GTGCGT…
##  3 Library prep 2 A10              CATCTTCT      PB-L021 TCATAT… 5Y D9.1 CATCTT…
##  4 Library prep 2 H11              CTAGCCGA      PB-L021 TCATAT… 6_1.39… CTAGCC…
##  5 Library prep 2 H10              ATGCCGCT      PB-L021 TCATAT… 5Y D15… ATGCCG…
##  6 Library prep 2 H09              CGCGTGAT      PB-L021 TCATAT… 5Y D6.3 CGCGTG…
##  7 Library prep 2 D09              TCCTTGGC      PB-L021 TCATAT… 5Y D3.2 TCCTTG…
##  8 Library prep 2 D12              TGGACAAC      PB-L021 TCATAT… 6_0.03… TGGACA…
##  9 Library prep 2 F09              CAGGCTTC      PB-L021 TCATAT… 5Y D6.1 CAGGCT…
## 10 Library prep 2 D11              CAACCGTG      PB-L021 TCATAT… 5Y D18… CAACCG…
## # … with 22 more rows, and abbreviated variable names ¹​`i7 Sequence*`,
## #   ²​`i5 Index Name`, ³​`i5 Sequence`, ⁴​Description, ⁵​sample.id
## # ℹ Use `print(n = ...)` to see more rows
## 
## $katelynp.metadata
## # A tibble: 25 × 7
##    `Pool Name*`   `i7 Index Name*` i7 Sequence…¹ i5 In…² i5 Se…³ Descr…⁴ sampl…⁵
##    <chr>          <chr>            <chr>         <chr>   <chr>   <chr>   <chr>  
##  1 Library prep 1 B07              CTCTCAGG      PB-L044 ATGTAT… MCF10A… CTCTCA…
##  2 Library prep 1 D07              TGCTCCGT      PB-L044 ATGTAT… MCF10A… TGCTCC…
##  3 Library prep 1 F07              ACCGTTCC      PB-L044 ATGTAT… MCF10A… ACCGTT…
##  4 Library prep 1 F01              CCGAGTTA      PB-L044 ATGTAT… MCF10A… CCGAGT…
##  5 Library prep 2 C03              AAGTACCT      PB-L021 TCATAT… MCF7_M… AAGTAC…
##  6 Library prep 2 E02              ACTCGAAT      PB-L021 TCATAT… MCF7_M… ACTCGA…
##  7 Library prep 2 C07              CACCGCAA      PB-L021 TCATAT… MCF7_M… CACCGC…
##  8 Library prep 2 F02              GTACCAGC      PB-L021 TCATAT… MCF7_M… GTACCA…
##  9 Library prep 2 C02              CAGGAAGG      PB-L021 TCATAT… MCF7_M… CAGGAA…
## 10 Library prep 1 E01              TGGTGACT      PB-L044 ATGTAT… MCF10A… TGGTGA…
## # … with 15 more rows, and abbreviated variable names ¹​`i7 Sequence*`,
## #   ²​`i5 Index Name`, ³​`i5 Sequence`, ⁴​Description, ⁵​sample.id
## # ℹ Use `print(n = ...)` to see more rows
## 
## $lindas.metadata
## # A tibble: 11 × 7
##    `Pool Name*`   `i7 Index Name*` i7 Sequence…¹ i5 In…² i5 Se…³ Descr…⁴ sampl…⁵
##    <chr>          <chr>            <chr>         <chr>   <chr>   <chr>   <chr>  
##  1 Library prep 2 H10              ATGCCGCT      PB-L021 TCATAT… 5Y D15… ATGCCG…
##  2 Library prep 1 D12              TGGACAAC      PB-L044 ATGTAT… 8590-V1 TGGACA…
##  3 Library prep 2 D11              CAACCGTG      PB-L021 TCATAT… 5Y D18… CAACCG…
##  4 Library prep 1 C12              GTTATCGA      PB-L044 ATGTAT… 8501-D1 GTTATC…
##  5 Library prep 2 F10              ACCGACCA      PB-L021 TCATAT… 5Y D12… ACCGAC…
##  6 Library prep 2 E10              CAACTCCG      PB-L021 TCATAT… 5Y D12… CAACTC…
##  7 Library prep 2 G10              GTGCGAGT      PB-L021 TCATAT… 5Y D15… GTGCGA…
##  8 Library prep 2 D10              CAGGCCAT      PB-L021 TCATAT… 5Y D12… CAGGCC…
##  9 Library prep 2 B11              ACGCTGCA      PB-L021 TCATAT… 5Y D18… ACGCTG…
## 10 Library prep 2 C11              CGATGGCA      PB-L021 TCATAT… 5Y D18… CGATGG…
## 11 Library prep 2 A11              TCCTCAGA      PB-L021 TCATAT… 5Y D15… TCCTCA…
## # … with abbreviated variable names ¹​`i7 Sequence*`, ²​`i5 Index Name`,
## #   ³​`i5 Sequence`, ⁴​Description, ⁵​sample.id

 

For an interactive paged table output, you will need to individually call on a specific list entry.¹ For example, let’s take a look at the paged table output of the Komen re-runs:

⊕NOTE: Multiple paged table interactive outputs w/ ‘show/hide’ buttons do not work due to the Javascript dependencies not being included in the HTML output. See footnotes for further details.

paged_table(split.metadata.list[[1]]) #list index for komen re-run experiment

Now that we’ve split the metadata according to experiment, let’s split the modified.counts using the split.metadata.list. Since we stored our split metadata in a list, we can efficiently generate our count matrix splits through recursion.

#Create an empty storage object for the split count matrices
split.counts <- c()

#To avoid using for loops, we use lapply to store the results in a list
split.counts <- lapply(split.metadata.list, function(x) {
    select(modified.counts, matches(x$sample.id))
})

#Match the order of the split.counts entries using the split.metadata.list
  #Use mapply when there are two or more lists needing recursion
split.counts <- mapply(function(x, y) 
  y[ ,match(x$sample.id, colnames(y))], split.metadata.list, split.counts)

#The list elements are named using the split.metadata.list
# Rename the list items to appropriately reflect the counts objects   
names(split.counts) <- gsub('.metadata', '.counts', names(split.counts))

 

⊕NOTE: The manual ‘sanity checks’ for each list element shown here are for illustrative purposes. We could’ve also done this in a loop too. Let’s confirm the split.counts were split properly according to the split.metadata.list.

# Check that the column names of the counts data matches 
# the values of the sample.id column in each experiment's metadata
all(split.metadata.list$komenredo.metadata$sample.id == colnames(split.counts$komenredo.metadata))
all(split.metadata.list$rachelm.metadata$sample.id == colnames(split.counts$rachelm.metadata))
all(split.metadata.list$katelynp.metadata$sample.id == colnames(split.counts$katelynp.metadata))
all(split.metadata.list$lindas.metadata$sample.id == colnames(split.counts$lindas.metadata))

## [1] TRUE

## [1] TRUE

## [1] TRUE

## [1] TRUE

Optional: Exporting to CSV

⊕NOTE: This function saves the created folders and files to wherever you saved this rmarkdown code. It is highly recommended to make a copy of these generated folders/files prior to editing or moving them. If you would like to share and analyze the curated data in excel, you can export the split lists to csv files:

#Be sure to set your working directory (or desired save folder) 
#before creating these files

#Create a custom function which creates folders and files 
#based on the list entry names
csv_export_function <- function(x) {  
  for(i in names(x)){
    dir.create(paste0(i, "folder"), showWarnings = FALSE)
    write.csv(x[[i]], file.path(paste0(i, "folder"), paste0(i,".csv"))
              )
    }
  }

# Generate folders and csv files
csv_export_function(split.counts)
csv_export_function(split.metadata.list)

2.5 DGEList Conversion

⊕NOTE: If you plan to use DESeq2 instead of edgeR for your differential gene expression analysis, check out the DEFormats package to convert between the formal object classes. To streamline downstream processing and gene set testing, the counts matrix can be converted into a DGEList-object using the DGEList function. This is an object used by edgeR to store the counts data, metadata, and other various experimental parameters (Robinson, McCarthy, and Smyth 2010).

split.DGElist <- lapply(split.counts, function(x) DGEList(x))

# Take a look at the DGELists
split.DGElist

## $komenredo.counts
## An object of class "DGEList"
## $counts
##            TTCCATTC.ATGTATCA TACAGAGT.ATGTATCA TCAAGGAT.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                   154               225               578
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CCACAATG.TCATATAT CTGGTCGT.TCATATAT ACACAACA.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   248               268               145
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CGCGTGAT.ATGTATCA TCCTATCT.TCATATAT AACCAATC.TCATATAT
## DDX11L1                    8                 0                 0
## WASH7P                   246               212               111
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            TCTATTGG.TCATATAT TTCACACT.ATGTATCA CGCTCTTG.ATGTATCA
## DDX11L1                    0                 0                 2
## WASH7P                   140               115               229
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            ACTCACCG.ATGTATCA TGGTACAG.TCATATAT CCTGTTAC.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   283               285               221
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CGCAACAG.ATGTATCA CTAGCCGA.ATGTATCA ACTCGAAT.ATGTATCA
## DDX11L1                    1                 0                 0
## WASH7P                   157               136               155
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            GATGAGAA.ATGTATCA CCTACACA.ATGTATCA ACCTGAGC.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                   250               143               145
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            AACGCTTG.TCATATAT CATCTTCT.ATGTATCA ATTCGCAG.TCATATAT
## DDX11L1                    0                 6                 0
## WASH7P                   262               278               159
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            GGTGTGAC.TCATATAT CGTAATTC.TCATATAT ACATCCTT.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   247               241               116
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CGATGGCA.ATGTATCA CCAGGTAA.ATGTATCA GTTAAGCA.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   190                98               148
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CTGTACGC.TCATATAT CTAACAAC.ATGTATCA TCAACTGA.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   174               204               165
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            GTTCGTCT.TCATATAT CCTTATGT.TCATATAT ATTCCGTA.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                   142               169                90
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CCGAGTTA.TCATATAT CTCGTACA.ATGTATCA TCCTCAGA.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                    92               239               143
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CGAGCATT.TCATATAT TGAATGTG.TCATATAT GGCTCCTA.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   345               117               100
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            TCAGATAC.TCATATAT CCATACTC.ATGTATCA TGAATGTG.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   183               158               149
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            AATGTGCC.ATGTATCA TGTAAGAC.TCATATAT GGAGCTAT.TCATATAT
## DDX11L1                    0                 0                 1
## WASH7P                   166                74                62
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CGCTCTTG.TCATATAT TGAACTCT.ATGTATCA AACGCTTG.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   261               230               292
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            ATGACACC.ATGTATCA TCACTCAC.ATGTATCA ATGGAACA.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   131               183                83
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            GTGCGAGT.ATGTATCA TGTTGCAC.ATGTATCA ACCGTTCC.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                   164               119               144
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CACATGGT.TCATATAT ATGGTCCG.ATGTATCA CTTGTTGG.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   306               105               352
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            ACGAAGCG.TCATATAT CCATTGCG.TCATATAT ATAGATCC.ATGTATCA
## DDX11L1                    0                 0                 8
## WASH7P                   235               237               186
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            ATTCCGTA.ATGTATCA CAGGCCAT.ATGTATCA CAGGCTTC.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                    85               139               232
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            TACAGAGT.TCATATAT ATGGTCCG.TCATATAT TTGGCTGC.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                   113               179               104
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CACAGTCT.ATGTATCA ACGCTGCA.ATGTATCA CGTAATTC.ATGTATCA
## DDX11L1                    2                 0                 0
## WASH7P                   132               182               174
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            TCTATTGG.ATGTATCA ACTCACCG.TCATATAT TCCTTGGC.ATGTATCA
## DDX11L1                    0                 2                 6
## WASH7P                    71                72               203
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            ACGAAGCG.ATGTATCA ATGCCGCT.ATGTATCA CAGAGTGG.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                   310               236                60
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CTGTACGC.ATGTATCA GTTCGTCT.ATGTATCA TTCACACT.TCATATAT
## DDX11L1                    2                 0                 0
## WASH7P                    90               135               226
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CAGGAAGG.ATGTATCA GTTAAGCA.TCATATAT GGCTCCTA.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                   209               168               141
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CTCGTACA.TCATATAT GGAGCTAT.ATGTATCA CGACTAGC.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   180                77               257
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            TCCTATCT.ATGTATCA TGGTACAG.ATGTATCA GTTGACAG.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   326               230               219
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CGACTAGC.TCATATAT GTACCAGC.ATGTATCA CCATTGCG.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   185               168               227
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CACAGTCT.TCATATAT CGTCTGAA.ATGTATCA CCACAATG.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   277                87               189
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CAAGTGAC.TCATATAT AAGTACCT.ATGTATCA CCTTATGT.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                    81               210               291
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CAGAAGAA.ATGTATCA CTTGTTGG.TCATATAT AACCAATC.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   114               222                88
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            ATTCTCCA.ATGTATCA ACTTCAAC.ATGTATCA CACATGGT.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                    84               136               306
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CAAGTAGT.ATGTATCA CTTCTGGC.ATGTATCA GGTGTGAC.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   282                62               164
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            TGAACTCT.TCATATAT TGGTGGAA.TCATATAT ATTCGCAG.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   220               172               240
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            TGTAAGAC.ATGTATCA GTGTCCAT.ATGTATCA CTAAGGCG.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   151               193               182
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CAACTCCG.ATGTATCA ACCTGAGC.ATGTATCA ACCGACCA.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   177               138               120
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CAACCGTG.ATGTATCA TCAGATAC.ATGTATCA TGGTGACT.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                   197               242               114
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            ATAGATCC.TCATATAT CCAGGTAA.TCATATAT CTGGTCGT.ATGTATCA
## DDX11L1                    0                 0                14
## WASH7P                   113               117               274
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
## 95561 more rows ...
## 
## $samples
##                   group lib.size norm.factors
## TTCCATTC.ATGTATCA     1 27215440            1
## TACAGAGT.ATGTATCA     1 30307669            1
## TCAAGGAT.TCATATAT     1 57944377            1
## CCACAATG.TCATATAT     1 36884641            1
## CTGGTCGT.TCATATAT     1 46858022            1
## 118 more rows ...
## 
## 
## $rachelm.counts
## An object of class "DGEList"
## $counts
##            GTTATCGA.TCATATAT GTGCGTTC.TCATATAT CATCTTCT.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                     0               960                28
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CTAGCCGA.TCATATAT ATGCCGCT.TCATATAT CGCGTGAT.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                   935               977              1535
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            TCCTTGGC.TCATATAT TGGACAAC.TCATATAT CAGGCTTC.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                   865               794              1345
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CAACCGTG.TCATATAT CTATTCCA.TCATATAT CAAGTAGT.TCATATAT
## DDX11L1                    0                 2                 0
## WASH7P                   924               947              1001
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            ACATCCTT.TCATATAT ACACAACA.TCATATAT ACCGACCA.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                   686                 0               956
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            GTGTCCAT.TCATATAT CTGCGAAC.TCATATAT CAACTCCG.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                   965              1046              1312
## MIR1302-11                 0                 4                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            GTGCGAGT.TCATATAT CAGGCCAT.TCATATAT TCACTCAC.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                   916              1090               968
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CCTACACA.TCATATAT CGCAACAG.TCATATAT CTTCTGGC.TCATATAT
## DDX11L1                    2                 0                 0
## WASH7P                   922                 0                 0
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CTAAGGCG.TCATATAT ACGCTGCA.TCATATAT TTCCATTC.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                     0                 0               816
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CCATACTC.TCATATAT CGATGGCA.TCATATAT TCCTCAGA.TCATATAT
## DDX11L1                    0                 4                 0
## WASH7P                     0               821               574
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            GCCAGTGT.TCATATAT TCAACTGA.TCATATAT
## DDX11L1                    0                 0
## WASH7P                   775               723
## MIR1302-11                 0                 0
## FAM138A                    0                 0
## OR4G4P                     0                 0
## 95561 more rows ...
## 
## $samples
##                   group lib.size norm.factors
## GTTATCGA.TCATATAT     1    87180            1
## GTGCGTTC.TCATATAT     1 48437668            1
## CATCTTCT.TCATATAT     1  4929321            1
## CTAGCCGA.TCATATAT     1 33486435            1
## ATGCCGCT.TCATATAT     1 45299550            1
## 27 more rows ...
## 
## 
## $katelynp.counts
## An object of class "DGEList"
## $counts
##            CTCTCAGG.ATGTATCA TGCTCCGT.ATGTATCA ACCGTTCC.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   303               487               198
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CCGAGTTA.ATGTATCA AAGTACCT.TCATATAT ACTCGAAT.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                   132               269               592
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CACCGCAA.TCATATAT GTACCAGC.TCATATAT CAGGAAGG.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                   295               258               170
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            TGGTGACT.ATGTATCA CACCGCAA.ATGTATCA TGCTCCGT.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                   246               201               296
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            TTGGCTGC.ATGTATCA CAAGTGAC.ATGTATCA GTTGACAG.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                   220               158               166
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            TCAAGGAT.ATGTATCA CAGAGTGG.ATGTATCA ACTTCAAC.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                   173               347               129
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            AATGTGCC.TCATATAT CGAGCATT.ATGTATCA CCTGTTAC.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                   189               383               174
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CGTCTGAA.TCATATAT TGGTGGAA.ATGTATCA CAGAAGAA.TCATATAT
## DDX11L1                    6                 0                 0
## WASH7P                   307               151               171
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CTCTCAGG.TCATATAT
## DDX11L1                    6
## WASH7P                   389
## MIR1302-11                 0
## FAM138A                    0
## OR4G4P                     0
## 95561 more rows ...
## 
## $samples
##                   group lib.size norm.factors
## CTCTCAGG.ATGTATCA     1 36202918            1
## TGCTCCGT.ATGTATCA     1 46517380            1
## ACCGTTCC.ATGTATCA     1 28132087            1
## CCGAGTTA.ATGTATCA     1 23739546            1
## AAGTACCT.TCATATAT     1 26601374            1
## 20 more rows ...
## 
## 
## $lindas.counts
## An object of class "DGEList"
## $counts
##            ATGCCGCT.TCATATAT TGGACAAC.ATGTATCA CAACCGTG.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                   977                 0               924
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            GTTATCGA.ATGTATCA ACCGACCA.TCATATAT CAACTCCG.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                     8               956              1312
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            GTGCGAGT.TCATATAT CAGGCCAT.TCATATAT ACGCTGCA.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                   916              1090                 0
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CGATGGCA.TCATATAT TCCTCAGA.TCATATAT
## DDX11L1                    4                 0
## WASH7P                   821               574
## MIR1302-11                 0                 0
## FAM138A                    0                 0
## OR4G4P                     0                 0
## 95561 more rows ...
## 
## $samples
##                   group lib.size norm.factors
## ATGCCGCT.TCATATAT     1 45299550            1
## TGGACAAC.ATGTATCA     1 53527697            1
## CAACCGTG.TCATATAT     1 42900281            1
## GTTATCGA.ATGTATCA     1 26280628            1
## ACCGACCA.TCATATAT     1 36032389            1
## 6 more rows ...

# Examine the slots stored in a DGEList
#  i.e. Komen re-run example
#  Note: 'split.DGElist[[1]]' index and 
#  '_split.DGElist$komenredo.counts_' refer to the same object
names(split.DGElist[[1]])

## [1] "counts"  "samples"

# Library size information is automatically generated 
# and stored in the $samples slot
#  i.e. Komen re-run example
split.DGElist[[1]]$samples

##                   group lib.size norm.factors
## TTCCATTC.ATGTATCA     1 27215440            1
## TACAGAGT.ATGTATCA     1 30307669            1
## TCAAGGAT.TCATATAT     1 57944377            1
## CCACAATG.TCATATAT     1 36884641            1
## CTGGTCGT.TCATATAT     1 46858022            1
## ACACAACA.ATGTATCA     1 27928252            1
## CGCGTGAT.ATGTATCA     1 39774754            1
## TCCTATCT.TCATATAT     1 41344487            1
## AACCAATC.TCATATAT     1 25213495            1
## TCTATTGG.TCATATAT     1 23026588            1
## TTCACACT.ATGTATCA     1 18270588            1
## CGCTCTTG.ATGTATCA     1 36144205            1
## ACTCACCG.ATGTATCA     1 31895776            1
## TGGTACAG.TCATATAT     1 57110606            1
## CCTGTTAC.ATGTATCA     1 30788834            1
## CGCAACAG.ATGTATCA     1 22667685            1
## CTAGCCGA.ATGTATCA     1 30369293            1
## ACTCGAAT.ATGTATCA     1 26020272            1
## GATGAGAA.ATGTATCA     1 27066847            1
## CCTACACA.ATGTATCA     1 25822978            1
## ACCTGAGC.TCATATAT     1 43083333            1
## AACGCTTG.TCATATAT     1 44302260            1
## CATCTTCT.ATGTATCA     1 32626325            1
## ATTCGCAG.TCATATAT     1 42273118            1
## GGTGTGAC.TCATATAT     1 47354423            1
## CGTAATTC.TCATATAT     1 41517718            1
## ACATCCTT.ATGTATCA     1 29082112            1
## CGATGGCA.ATGTATCA     1 30879570            1
## CCAGGTAA.ATGTATCA     1 20604597            1
## GTTAAGCA.ATGTATCA     1 24253690            1
## CTGTACGC.TCATATAT     1 35268858            1
## CTAACAAC.ATGTATCA     1 24999988            1
## TCAACTGA.ATGTATCA     1 32864745            1
## GTTCGTCT.TCATATAT     1 29035353            1
## CCTTATGT.TCATATAT     1 42051531            1
## ATTCCGTA.TCATATAT     1 15435111            1
## CCGAGTTA.TCATATAT     1 42290802            1
## CTCGTACA.ATGTATCA     1 33566440            1
## TCCTCAGA.ATGTATCA     1 27836054            1
## CGAGCATT.TCATATAT     1 25839369            1
## TGAATGTG.TCATATAT     1 25589726            1
## GGCTCCTA.ATGTATCA     1 15860851            1
## TCAGATAC.TCATATAT     1 43896958            1
## CCATACTC.ATGTATCA     1 23087529            1
## TGAATGTG.ATGTATCA     1 24227588            1
## AATGTGCC.ATGTATCA     1 27260902            1
## TGTAAGAC.TCATATAT     1 15730498            1
## GGAGCTAT.TCATATAT     1 35409237            1
## CGCTCTTG.TCATATAT     1 51687944            1
## TGAACTCT.ATGTATCA     1 26648861            1
## AACGCTTG.ATGTATCA     1 33958777            1
## ATGACACC.ATGTATCA     1 24721224            1
## TCACTCAC.ATGTATCA     1 30176672            1
## ATGGAACA.ATGTATCA     1 20899919            1
## GTGCGAGT.ATGTATCA     1 36536116            1
## TGTTGCAC.ATGTATCA     1 27843244            1
## ACCGTTCC.TCATATAT     1 14587009            1
## CACATGGT.TCATATAT     1 46398149            1
## ATGGTCCG.ATGTATCA     1 21204194            1
## CTTGTTGG.ATGTATCA     1 47156292            1
## ACGAAGCG.TCATATAT     1 48752353            1
## CCATTGCG.TCATATAT     1 40573019            1
## ATAGATCC.ATGTATCA     1 28901973            1
## ATTCCGTA.ATGTATCA     1 20503593            1
## CAGGCCAT.ATGTATCA     1 32907729            1
## CAGGCTTC.ATGTATCA     1 34383939            1
## TACAGAGT.TCATATAT     1 22634148            1
## ATGGTCCG.TCATATAT     1 40165698            1
## TTGGCTGC.TCATATAT     1 31579865            1
## CACAGTCT.ATGTATCA     1 21841823            1
## ACGCTGCA.ATGTATCA     1 40472957            1
## CGTAATTC.ATGTATCA     1 26967394            1
## TCTATTGG.ATGTATCA     1 17648956            1
## ACTCACCG.TCATATAT     1 46566485            1
## TCCTTGGC.ATGTATCA     1 31927477            1
## ACGAAGCG.ATGTATCA     1 37894492            1
## ATGCCGCT.ATGTATCA     1 37768945            1
## CAGAGTGG.TCATATAT     1 13824535            1
## CTGTACGC.ATGTATCA     1 21248733            1
## GTTCGTCT.ATGTATCA     1 28986090            1
## TTCACACT.TCATATAT     1 36459215            1
## CAGGAAGG.ATGTATCA     1 26263405            1
## GTTAAGCA.TCATATAT     1 27486372            1
## GGCTCCTA.TCATATAT     1 31620592            1
## CTCGTACA.TCATATAT     1 28801440            1
## GGAGCTAT.ATGTATCA     1 19220820            1
## CGACTAGC.ATGTATCA     1 39703781            1
## TCCTATCT.ATGTATCA     1 40296811            1
## TGGTACAG.ATGTATCA     1 44027683            1
## GTTGACAG.ATGTATCA     1 33602172            1
## CGACTAGC.TCATATAT     1 34162718            1
## GTACCAGC.ATGTATCA     1 26839443            1
## CCATTGCG.ATGTATCA     1 31393521            1
## CACAGTCT.TCATATAT     1 54345484            1
## CGTCTGAA.ATGTATCA     1 19396527            1
## CCACAATG.ATGTATCA     1 29580264            1
## CAAGTGAC.TCATATAT     1 16922959            1
## AAGTACCT.ATGTATCA     1 33034193            1
## CCTTATGT.ATGTATCA     1 35220520            1
## CAGAAGAA.ATGTATCA     1 14372483            1
## CTTGTTGG.TCATATAT     1 48024206            1
## AACCAATC.ATGTATCA     1 16943604            1
## ATTCTCCA.ATGTATCA     1 18834217            1
## ACTTCAAC.ATGTATCA     1 20712225            1
## CACATGGT.ATGTATCA     1 34541302            1
## CAAGTAGT.ATGTATCA     1 36174411            1
## CTTCTGGC.ATGTATCA     1 18276182            1
## GGTGTGAC.ATGTATCA     1 38683395            1
## TGAACTCT.TCATATAT     1 50468199            1
## TGGTGGAA.TCATATAT     1 33917978            1
## ATTCGCAG.ATGTATCA     1 31750310            1
## TGTAAGAC.ATGTATCA     1 18707018            1
## GTGTCCAT.ATGTATCA     1 35573361            1
## CTAAGGCG.ATGTATCA     1 35583706            1
## CAACTCCG.ATGTATCA     1 26514035            1
## ACCTGAGC.ATGTATCA     1 35296206            1
## ACCGACCA.ATGTATCA     1 22024497            1
## CAACCGTG.ATGTATCA     1 40892786            1
## TCAGATAC.ATGTATCA     1 32716083            1
## TGGTGACT.TCATATAT     1 42517838            1
## ATAGATCC.TCATATAT     1 44423154            1
## CCAGGTAA.TCATATAT     1 26361557            1
## CTGGTCGT.ATGTATCA     1 39910028            1

2.5.1 Storing sample metadata

The DGEList object is also able to store and associate metadata for the samples, aka our column names for the counts matrix. Since we previously matched the names and order of the split.metadata.list, we can store the group design factors for samples in $samples$group.

For this example, we will modify the split.metadata.list entry for the Komen re-run experiment in order to streamline DGEList storage. We perform pattern matching on the $Description column to create our columns for the experimental design factors.

#Here we directly reference the entry name  
split.metadata.list[["komenredo.metadata"]] <- 
  split.metadata.list[["komenredo.metadata"]] %>%
  #Create a column for patient cell-line groups
  mutate(Sample = case_when(
    
    grepl("7518", .$Description) ~ 'KCR7518',
    grepl("7889", .$Description) ~ 'KCR7889',
    grepl("7953", .$Description) ~ 'KCR7953',
    grepl("8195", .$Description) ~ 'KCR8195',
    grepl("8519", .$Description) ~ 'KCR8519',
    grepl("8580", .$Description) ~ 'KCR8580',
    
  )) %>% 
  
  #Create a column for chemical treatments
  # Note: All chemicals did not require a re-run,
  # but are referenced here just in case
  mutate(Treatment = case_when(
    
    #Water-controlled chemicals
    grepl("Water", .$Description) ~ 'Water',
    grepl("Cadmium Chloride", .$Description) ~ 'Cadmium_Chloride',
    grepl("Copper Chloride", .$Description) ~ 'Copper_Chloride',
    grepl("Sodium Arsenite", .$Description) ~ 'Sodium_Arsenite',
    grepl("Lead Acetate", .$Description) ~ 'Lead_Acetate',
    
    #DMSO-controlled chemicals
    grepl("DMSO", .$Description) ~ 'DMSO',
    grepl("DDE", .$Description) ~ 'DDE',
    grepl("BPS", .$Description) ~ 'BPS',
    grepl("BPA", .$Description) ~ 'BPA',
    grepl("PFNA", .$Description) ~ 'PFNA',
  )) %>% 

  #Create a column for dose
  # Note: Water and DMSO are dose 0 uM for 
  # chemical classes
  mutate(Dose = case_when(

    grepl(paste(c("Water","DMSO"), collapse = "|"),
                 .$Description) ~ '0',
    grepl("0.1uM", .$Description) ~ '0.1',
    grepl("1uM", .$Description) ~ '1',
    grepl("10uM", .$Description) ~ '10'
    
  )) %>% 
  
  #Create a column for design matrix contrast factor levels
  # Note: The design and contrast matrices 
  #       are not covered in this pipeline,
  #       but are here for reference
  
  mutate(cf_level = paste0(.$Sample, sep = "_", 
                           .$Treatment, sep = "_", 
                           .$Dose))

Take a look at the modified split.metadata.list[["komenredo.metadata"]]:

split.metadata.list[["komenredo.metadata"]]

Now, we can store these modified metadata columns in the $samples tab of the DGEList:

# Store patient cell-line groups into the DGEList
split.DGElist$komenredo.counts$samples$group <- 
  #Be sure to convert your strings as factors
  as.factor(split.metadata.list[["komenredo.metadata"]]$Sample)

# Store chemical treatments into the DGEList
split.DGElist$komenredo.counts$samples$treatment <- 
  #Be sure to convert your strings as factors
  as.factor(split.metadata.list[["komenredo.metadata"]]$Treatment)

# Store chemical doses into the DGEList
split.DGElist$komenredo.counts$samples$dose <- 
  #Be sure to convert your strings as factors
  as.factor(split.metadata.list[["komenredo.metadata"]]$Dose)

#Take a look at the added DGEList $samples information
split.DGElist$komenredo.counts$samples

##                     group lib.size norm.factors        treatment dose
## TTCCATTC.ATGTATCA KCR8580 27215440            1             PFNA   10
## TACAGAGT.ATGTATCA KCR7953 30307669            1              DDE  0.1
## TCAAGGAT.TCATATAT KCR8195 57944377            1             DMSO    0
## CCACAATG.TCATATAT KCR7889 36884641            1              BPS  0.1
## CTGGTCGT.TCATATAT KCR7889 46858022            1              BPS   10
## ACACAACA.ATGTATCA KCR8580 27928252            1              BPA    1
## CGCGTGAT.ATGTATCA KCR8580 39774754            1              BPA  0.1
## TCCTATCT.TCATATAT KCR7889 41344487            1              BPA   10
## AACCAATC.TCATATAT KCR7889 25213495            1              BPA  0.1
## TCTATTGG.TCATATAT KCR7889 23026588            1              BPA    1
## TTCACACT.ATGTATCA KCR7953 18270588            1              BPS   10
## CGCTCTTG.ATGTATCA KCR7953 36144205            1             PFNA   10
## ACTCACCG.ATGTATCA KCR7953 31895776            1             DMSO    0
## TGGTACAG.TCATATAT KCR7889 57110606            1             PFNA   10
## CCTGTTAC.ATGTATCA KCR7953 30788834            1              BPA   10
## CGCAACAG.ATGTATCA KCR8580 22667685            1              BPS  0.1
## CTAGCCGA.ATGTATCA KCR8580 30369293            1             PFNA   10
## ACTCGAAT.ATGTATCA KCR7953 26020272            1              BPA    1
## GATGAGAA.ATGTATCA KCR8580 27066847            1             DMSO    0
## CCTACACA.ATGTATCA KCR8580 25822978            1              BPA  0.1
## ACCTGAGC.TCATATAT KCR7889 43083333            1             PFNA  0.1
## AACGCTTG.TCATATAT KCR7889 44302260            1             PFNA   10
## CATCTTCT.ATGTATCA KCR8580 32626325            1              BPA  0.1
## ATTCGCAG.TCATATAT KCR7889 42273118            1             PFNA  0.1
## GGTGTGAC.TCATATAT KCR7889 47354423            1              BPS  0.1
## CGTAATTC.TCATATAT KCR7889 41517718            1             PFNA  0.1
## ACATCCTT.ATGTATCA KCR8580 29082112            1              BPA    1
## CGATGGCA.ATGTATCA KCR8580 30879570            1             PFNA  0.1
## CCAGGTAA.ATGTATCA KCR7953 20604597            1             PFNA  0.1
## GTTAAGCA.ATGTATCA KCR7953 24253690            1              BPS  0.1
## CTGTACGC.TCATATAT KCR7518 35268858            1             DMSO    0
## CTAACAAC.ATGTATCA KCR8580 24999988            1              BPS    1
## TCAACTGA.ATGTATCA KCR8580 32864745            1             PFNA    1
## GTTCGTCT.TCATATAT KCR7889 29035353            1             PFNA    1
## CCTTATGT.TCATATAT KCR7518 42051531            1              BPA  0.1
## ATTCCGTA.TCATATAT KCR7889 15435111            1             PFNA   10
## CCGAGTTA.TCATATAT KCR7518 42290802            1              BPS   10
## CTCGTACA.ATGTATCA KCR7953 33566440            1              DDE    1
## TCCTCAGA.ATGTATCA KCR8580 27836054            1              DDE   10
## CGAGCATT.TCATATAT KCR8195 25839369            1  Sodium_Arsenite   10
## TGAATGTG.TCATATAT KCR7889 25589726            1              BPA    1
## GGCTCCTA.ATGTATCA KCR7953 15860851            1            Water    0
## TCAGATAC.TCATATAT KCR7889 43896958            1              BPS    1
## CCATACTC.ATGTATCA KCR8580 23087529            1              BPS    1
## TGAATGTG.ATGTATCA KCR7953 24227588            1              BPS    1
## AATGTGCC.ATGTATCA KCR7953 27260902            1              BPA   10
## TGTAAGAC.TCATATAT KCR7889 15730498            1              BPS   10
## GGAGCTAT.TCATATAT KCR7518 35409237            1              BPA    1
## CGCTCTTG.TCATATAT KCR7889 51687944            1             DMSO    0
## TGAACTCT.ATGTATCA KCR7953 26648861            1             PFNA   10
## AACGCTTG.ATGTATCA KCR7953 33958777            1             PFNA    1
## ATGACACC.ATGTATCA KCR8580 24721224            1             DMSO    0
## TCACTCAC.ATGTATCA KCR8580 30176672            1              BPS   10
## ATGGAACA.ATGTATCA KCR8580 20899919            1              BPS    1
## GTGCGAGT.ATGTATCA KCR8580 36536116            1              BPA   10
## TGTTGCAC.ATGTATCA KCR8580 27843244            1             DMSO    0
## ACCGTTCC.TCATATAT KCR8195 14587009            1  Sodium_Arsenite   10
## CACATGGT.TCATATAT KCR7889 46398149            1              BPS  0.1
## ATGGTCCG.ATGTATCA KCR7953 21204194            1              BPS   10
## CTTGTTGG.ATGTATCA KCR7953 47156292            1              DDE  0.1
## ACGAAGCG.TCATATAT KCR7889 48752353            1             DMSO    0
## CCATTGCG.TCATATAT KCR7889 40573019            1              BPA    1
## ATAGATCC.ATGTATCA KCR7953 28901973            1             DMSO    0
## ATTCCGTA.ATGTATCA KCR7953 20503593            1             PFNA    1
## CAGGCCAT.ATGTATCA KCR8580 32907729            1              BPA    1
## CAGGCTTC.ATGTATCA KCR8580 34383939            1              BPS   10
## TACAGAGT.TCATATAT KCR7889 22634148            1              BPS    1
## ATGGTCCG.TCATATAT KCR7889 40165698            1              BPA   10
## TTGGCTGC.TCATATAT KCR8519 31579865            1             DMSO    0
## CACAGTCT.ATGTATCA KCR7953 21841823            1             PFNA  0.1
## ACGCTGCA.ATGTATCA KCR8580 40472957            1             PFNA  0.1
## CGTAATTC.ATGTATCA KCR7953 26967394            1              DDE   10
## TCTATTGG.ATGTATCA KCR7953 17648956            1              BPS    1
## ACTCACCG.TCATATAT KCR7518 46566485            1              BPA  0.1
## TCCTTGGC.ATGTATCA KCR8580 31927477            1              BPS   10
## ACGAAGCG.ATGTATCA KCR7953 37894492            1             PFNA   10
## ATGCCGCT.ATGTATCA KCR8580 37768945            1              DDE   10
## CAGAGTGG.TCATATAT KCR8519 13824535            1  Sodium_Arsenite   10
## CTGTACGC.ATGTATCA KCR7953 21248733            1            Water    0
## GTTCGTCT.ATGTATCA KCR7953 28986090            1             PFNA  0.1
## TTCACACT.TCATATAT KCR7889 36459215            1              BPA   10
## CAGGAAGG.ATGTATCA KCR7953 26263405            1              BPA  0.1
## GTTAAGCA.TCATATAT KCR7889 27486372            1              BPA  0.1
## GGCTCCTA.TCATATAT KCR7518 31620592            1             DMSO    0
## CTCGTACA.TCATATAT KCR7889 28801440            1              BPS   10
## GGAGCTAT.ATGTATCA KCR7953 19220820            1             DMSO    0
## CGACTAGC.ATGTATCA KCR7953 39703781            1              BPS  0.1
## TCCTATCT.ATGTATCA KCR7953 40296811            1 Cadmium_Chloride  0.1
## TGGTACAG.ATGTATCA KCR7953 44027683            1             PFNA    1
## GTTGACAG.ATGTATCA KCR7953 33602172            1              BPA   10
## CGACTAGC.TCATATAT KCR7889 34162718            1              BPA  0.1
## GTACCAGC.ATGTATCA KCR7953 26839443            1              BPA    1
## CCATTGCG.ATGTATCA KCR7953 31393521            1              BPS   10
## CACAGTCT.TCATATAT KCR7889 54345484            1             PFNA    1
## CGTCTGAA.ATGTATCA KCR7953 19396527            1              BPA  0.1
## CCACAATG.ATGTATCA KCR7953 29580264            1 Cadmium_Chloride   10
## CAAGTGAC.TCATATAT KCR8519 16922959            1  Sodium_Arsenite   10
## AAGTACCT.ATGTATCA KCR7953 33034193            1              BPS  0.1
## CCTTATGT.ATGTATCA KCR7953 35220520            1             DMSO    0
## CAGAAGAA.ATGTATCA KCR7953 14372483            1              BPA  0.1
## CTTGTTGG.TCATATAT KCR7889 48024206            1              BPS    1
## AACCAATC.ATGTATCA KCR7953 16943604            1              BPS    1
## ATTCTCCA.ATGTATCA KCR8580 18834217            1              BPS  0.1
## ACTTCAAC.ATGTATCA KCR7953 20712225            1              BPA    1
## CACATGGT.ATGTATCA KCR7953 34541302            1 Cadmium_Chloride  0.1
## CAAGTAGT.ATGTATCA KCR8580 36174411            1             PFNA    1
## CTTCTGGC.ATGTATCA KCR8580 18276182            1              BPS  0.1
## GGTGTGAC.ATGTATCA KCR7953 38683395            1 Cadmium_Chloride   10
## TGAACTCT.TCATATAT KCR7889 50468199            1             DMSO    0
## TGGTGGAA.TCATATAT KCR7518 33917978            1              BPS   10
## ATTCGCAG.ATGTATCA KCR7953 31750310            1              DDE   10
## TGTAAGAC.ATGTATCA KCR7953 18707018            1              DDE    1
## GTGTCCAT.ATGTATCA KCR8580 35573361            1             PFNA    1
## CTAAGGCG.ATGTATCA KCR8580 35583706            1             PFNA   10
## CAACTCCG.ATGTATCA KCR8580 26514035            1              BPA   10
## ACCTGAGC.ATGTATCA KCR7953 35296206            1              DDE   10
## ACCGACCA.ATGTATCA KCR8580 22024497            1              BPA   10
## CAACCGTG.ATGTATCA KCR8580 40892786            1             PFNA  0.1
## TCAGATAC.ATGTATCA KCR7953 32716083            1              DDE  0.1
## TGGTGACT.TCATATAT KCR7518 42517838            1              BPA    1
## ATAGATCC.TCATATAT KCR7518 44423154            1              BPA  0.1
## CCAGGTAA.TCATATAT KCR7889 26361557            1             PFNA    1
## CTGGTCGT.ATGTATCA KCR7953 39910028            1              DDE    1

Let’s double check that the stored row names of the metadata $samples information in the DGEList matches exactly to our column names of the counts data.

all(rownames(rownames(split.DGElist$komenredo.counts$samples)) 
    == colnames(split.counts$komenredo.counts))

## [1] TRUE

 

For the Komen re-runs experiment, we were also concerned about the library size, the total number of sequenced read counts that were mapped to our human reference genome. Let’s double check to see if our sample re-runs passed the coverage threshold of 5 million reads (\(\geq\) 5E06):

#Check to see if all samples passed the sequencing depth cutoff
all(split.DGElist[["komenredo.counts"]]$samples$lib.size >= 5000000)

## [1] TRUE

2.5.2 Storing gene annotations

Similar to how we stored sample information in the DGEList, we can also store gene-level information as well, aka the row names of our counts matrix. Currently, the only annotations we have in the DGEList counts matrix are the official gene id symbols (i.e. Human Genome Organisation (HUGO)).

 

Let’s add more informative gene information. For our demonstration, we will continue to use the Komen re-run example and the AnnotationDbi - org.Hs.eg.db packages.² This is a human gene annotation database since we are querying human genes.

⊕
NOTE: Be sure to use the correct gene annotation package for your experimental species. First, let’s take a look at the information we want to retrieve. In order to see what information is available from the annotations database, run the columns function:

columns(org.Hs.eg.db)

##  [1] "ACCNUM"       "ALIAS"        "ENSEMBL"      "ENSEMBLPROT"  "ENSEMBLTRANS"
##  [6] "ENTREZID"     "ENZYME"       "EVIDENCE"     "EVIDENCEALL"  "GENENAME"    
## [11] "GENETYPE"     "GO"           "GOALL"        "IPI"          "MAP"         
## [16] "OMIM"         "ONTOLOGY"     "ONTOLOGYALL"  "PATH"         "PFAM"        
## [21] "PMID"         "PROSITE"      "REFSEQ"       "SYMBOL"       "UCSCKG"      
## [26] "UNIPROT"

⊕NOTE: You will need to open and run this in R to see the help page. As you’ll see, there is a lot of annotation information to choose from. If you want to learn more about the values for each of these columns, enter the help command in your R console . It will pull up a manual describing what the fields mean.

#Example: Consult the help page to learn what "OMIM" is
help("OMIM")

For our komen re-run example, we will retrieve the following information³: ⊕Warning: The more information you want to retrieve, the more resource-intensive this operation becomes. Make sure you have enough allocation for memory and CPU resources, especially when retrieving multi-mapping information like ‘ONTOLOGY’.

• Commonly used unique gene IDs
  • “ENSEMBL”
  • “ENTREZID”
• Descriptive Info
  • “GENENAME”

When we retrieve information from the AnnotationDbi database, we need to specify what information we are using as our ‘query key’. In our Komen re-run example, this information would be our gene ID symbols used as the count rownames, aka SYMBOL. You can also use other information as the keytypes depending on the database and the information you have available.

⊕Tip: When choosing your keytypes, it is recommended to choose a bijective input. For example, ‘ENSEMBL’ ids are usually one-to-one matches, whereas keytypes such as ‘ONTOLOGYALL’ or ‘PATH’ are non-specific.

#Use this to see the list of keytypes 
#available for your Annotation.Dbi database
keytypes(org.Hs.eg.db)

 

We’ll convert the gene id symbols to retrieve the data we want to extract. ⊕NOTE: In our example, the gene rownames (i.e. keys) are actually the same as the original ‘modified.counts’ object. However, if you already filtered and omitted genes prior, you would need to reference the rownames of the specific object as shown in the code.

#Specify the database to query from 
annot.gene.ids <- AnnotationDbi::select(org.Hs.eg.db, 
       #Identify which genes you want to retrieve info on 
       keys = rownames(split.DGElist[["komenredo.counts"]]$counts),
       #Specify the type of input format for the gene ids from above
       keytype = 'SYMBOL',
       #Identify what information you want to retrieve
       column = c('ENSEMBL', 'ENTREZID', 'GENENAME') 
       )

## 'select()' returned 1:many mapping between keys and columns

You will notice the output returns the following statement: “‘select()’ returned 1:many mapping between keys and columns”

⊕NOTE: For instance, a single Entrez ID can have multiple gene names on one or more chromsomes/chromosome strands. See this post for further details. If this message occurs, we cannot directly add the annotation information into the genes slot of the DGEList just yet. This is because some of the gene-level information retrieved has multiple entries when mapping between the keys (i.e. genes from count rownames) and the columns (i.e. Entrez IDs, ENSEMBL IDs, gene names) (Phipson et al. 2020).

Before removing the duplicated gene IDs, be sure to review the duplicated gene IDs and understand the reason for duplication.

#Duplicated gene IDs
annot.gene.ids %>% 
  .[duplicated(.$SYMBOL), ]

##                SYMBOL         ENSEMBL  ENTREZID
## 170             PLCH2 ENSG00000276429      9651
## 174             PANK4 ENSG00000273494     55229
## 176              HES5 ENSG00000273529    388585
## 180          TNFRSF14 ENSG00000273936      8764
## 185             MMEL1 ENSG00000277131     79258
## 188             TTC34 ENSG00000275571 100287898
## 426          PRAMEF11 ENSG00000281934    440560
## 429          HNRNPCL1 ENSG00000282175    343069
## 431           PRAMEF2 ENSG00000282817     65122
## 433           PRAMEF4 ENSG00000282584    400735
## 435          PRAMEF10 ENSG00000282663    343071
## 437           PRAMEF7 ENSG00000279195    441871
## 441           PRAMEF6 ENSG00000282119    440561
## 448          PRAMEF25 ENSG00000276299    441873
## 449          PRAMEF25 ENSG00000282566    441873
## 450          PRAMEF25 ENSG00000283348    441873
## 457          PRAMEF26 ENSG00000276299    645359
## 458          PRAMEF26 ENSG00000282566    645359
## 459          PRAMEF26 ENSG00000281987    645359
## 460          PRAMEF26 ENSG00000283348    645359
## 461          PRAMEF26 ENSG00000283216    645359
## 462          PRAMEF26 ENSG00000229571    645359
## 466           PRAMEF5 ENSG00000276420    343068
## 467           PRAMEF5 ENSG00000282424    343068
## 468           PRAMEF5 ENSG00000283150    343068
## 472           PRAMEF8 ENSG00000278021    391002
## 473           PRAMEF8 ENSG00000282583    391002
## 474           PRAMEF8 ENSG00000283387    391002
## 477           PRAMEF9 ENSG00000281573    343070
## 478           PRAMEF9 ENSG00000282298    343070
## 479           PRAMEF9 ENSG00000283139    343070
## 482          PRAMEF13 ENSG00000282741    400736
## 484          PRAMEF18 ENSG00000277853    391003
## 485          PRAMEF18 ENSG00000282212    391003
## 608             PADI1 ENSG00000281459     29943
## 610             PADI3 ENSG00000280549     51702
## 612           MIR3972 ENSG00000281810 100616188
## 614             PADI4 ENSG00000280908     23569
## 617             PADI6 ENSG00000280949    353238
## 620              RCC2 ENSG00000281540     55920
## 765            HNRNPR ENSG00000282958     10236
## 767            ZNF436 ENSG00000283009     80818
## 771             TCEA3 ENSG00000282941      6920
## 774             ASAP3 ENSG00000282854     55616
## 776              E2F2 ENSG00000282899      1870
## 779               ID3 ENSG00000283060      3399
## 890           RPS6KA1 ENSG00000281877      6195
## 892           MIR1976 ENSG00000280948 100302190
## 968            DNAJC8 ENSG00000285317     22826
## 975             SESN2 ENSG00000285069     83667
## 977             MED18 ENSG00000284944     54797
## 1320            FOXO6 ENSG00000204060 100132074
## 2433         VAV3-AS1 ENSG00000284539 100873946
## 2437         SLC25A24 ENSG00000284468     29957
## 2597          SLC16A1 ENSG00000281917      6566
## 2971          PPIAL4F ENSG00000275974    728945
## 3247            INTS3 ENSG00000262826     65123
## 3251          SLC27A3 ENSG00000263163     11000
## 3254          GATAD2B ENSG00000261992     57459
## 3334              GBA ENSG00000262446      2629
## 3337          FAM189B ENSG00000262666     10712
## 3339           SCAMP3 ENSG00000263290     10067
## 3341             CLK2 ENSG00000261893      1196
## 3343             HCN3 ENSG00000263324     57657
## 3345             PKLR ENSG00000262785      5313
## 3659             RGS5 ENSG00000232995      8490
## 3932           SEC16B ENSG00000254154     89866
## 3977          FAM163A ENSG00000243062    148753
## 4210         ATP6V1G3 ENSG00000263014    127124
## 4213            PTPRC ENSG00000262418      5788
## 4498          SERTAD4 ENSG00000281230     56256
## 4502             HHAT ENSG00000280680     55733
## 4819           TRIM17 ENSG00000285344     51127
## 4825         MIR4666A ENSG00000284998 100616308
## 4828           RNF187 ENSG00000285426    149603
## 4833           RNA5S1 ENSG00000285166 100169751
## 4835           RNA5S2 ENSG00000285285 100169753
## 4837           RNA5S3 ENSG00000285168 100169754
## 4847          RNA5S12 ENSG00000285168 100169763
## 4848          RNA5S12 ENSG00000199337 100169763
## 4853          RNA5S16 ENSG00000284853 100169767
## 4855          RNA5S17 ENSG00000285158 100169768
## 4859             RHOU ENSG00000284984     58480
## 4995             TBCE ENSG00000282984      6905
## 4996             TBCE ENSG00000285053      6905
## 5000         B3GALNT2 ENSG00000282880    148789
## 5009             GNG4 ENSG00000282972      2786
## 5091             OPN3 ENSG00000203668     23596
## 5121           CEP170 ENSG00000276725      9859
## 5126          SDCCAG8 ENSG00000276111     10806
## 5130             AKT3 ENSG00000275199     10000
## 5163           KIF26B ENSG00000281216     55083
## 5261            OR2T4 ENSG00000275617    127074
## 5262            OR2T4 ENSG00000274870    127074
## 5264            OR2T6 ENSG00000278659    254879
## 5265            OR2T6 ENSG00000278689    254879
## 5267            OR2T1 ENSG00000273508     26696
## 5268            OR2T1 ENSG00000275244     26696
## 5270            OR2T7 ENSG00000281489     81458
## 5271            OR2T7 ENSG00000281395     81458
## 5273            OR2T2 ENSG00000275754    401992
## 5274            OR2T2 ENSG00000276821    401992
## 5276            OR2T3 ENSG00000277113    343173
## 5277            OR2T3 ENSG00000278377    343173
## 5280            OR2T5 ENSG00000275102    401993
## 5281            OR2T5 ENSG00000273827    401993
## 5332            SNTG2 ENSG00000281020     54221
## 5333            SNTG2 ENSG00000281486     54221
## 5338              TPO ENSG00000277603      7173
## 5357         TRAPPC12 ENSG00000274891     51112
## 5361             ADI1 ENSG00000280830     55256
## 5831            MEMO1 ENSG00000162959     51072
## 5850        LINC00486 ENSG00000236854    285045
## 5883            CRIM1 ENSG00000277354     51232
## 6400           ASPRV1 ENSG00000244617    151516
## 6862         ACTR3BP2 ENSG00000280263    440888
## 7308         RPL23AP7 ENSG00000184319    118433
## 7765            KIF5C ENSG00000276734      3800
## 7883            BAZ2B ENSG00000226266     29994
## 7983          NOSTRIN ENSG00000275326    115677
## 7985            SPC25 ENSG00000277909     57405
## 7987            G6PC2 ENSG00000278373     57818
## 7989           ABCB11 ENSG00000276582      8647
## 8021           ERICH2 ENSG00000239467    285141
## 8546           INO80D ENSG00000283510     54891
## 8550           NDUFS1 ENSG00000283447      4719
## 8554           EEF1B2 ENSG00000283391      1933
## 8557          SNORA41 ENSG00000283482    619569
## 8564            ZDBF2 ENSG00000283649     57683
## 8603          PLEKHM3 ENSG00000285005    389072
## 8611            CRYGD ENSG00000285434      1421
## 8613            CRYGC ENSG00000285011      1420
## 9027           INPP5D ENSG00000281614      3635
## 9030          ATG16L1 ENSG00000281089     55054
## 9032          SCARNA5 ENSG00000280652    677775
## 9034          SCARNA6 ENSG00000281388    677772
## 9036              SAG ENSG00000281857      6295
## 9039             DGKD ENSG00000280873      8527
## 9140           TWIST2 ENSG00000288335    117581
## 9227          GAL3ST2 ENSG00000276126     64090
## 9231             NEU4 ENSG00000277926    129807
## 9234            PDCD1 ENSG00000276977      5133
## 9402           TAMM41 ENSG00000279643    132001
## 9512            PLCL2 ENSG00000284017     23228
## 9514          MIR3714 ENSG00000283960 100500913
## 9881           ZNF445 ENSG00000283034    353274
## 9883           ZNF852 ENSG00000281626    285346
## 9887          ZKSCAN7 ENSG00000281894     55888
## 9891           ZNF660 ENSG00000280661    285349
## 9894           ZNF197 ENSG00000281709     10168
## 9896       ZNF197-AS1 ENSG00000280907 100874094
## 9898            ZNF35 ENSG00000281306      7584
## 9902           ZNF502 ENSG00000281448     91392
## 9904           ZNF501 ENSG00000281661    115560
## 9906         KIAA1143 ENSG00000281665     57456
## 9908            KIF15 ENSG00000280610     56992
## 9911           TMEM42 ENSG00000280516    131616
## 9913           MIR564 ENSG00000284275    693149
## 9915             TGM4 ENSG00000281886      7047
## 10118        CYB561D2 ENSG00000271858     11068
## 10350           MAGI1 ENSG00000282956      9223
## 10360        SLC25A26 ENSG00000282739    115286
## 10424            RYBP ENSG00000281766     23429
## 10466         FAM86DP ENSG00000288323    692099
## 10527       LINC00971 ENSG00000284871    440970
## 10582       LINC00879 ENSG00000285436    255025
## 10782         C3orf52 ENSG00000285394     79669
## 10785           GCSAM ENSG00000284925    257144
## 10788          SLC9C1 ENSG00000285044    285335
## 10817          SPICE1 ENSG00000285943    152185
## 11066          RUVBL1 ENSG00000284901      8607
## 11071          EEFSEC ENSG00000284869     60678
## 11219           CEP63 ENSG00000288700     80254
## 11495         AADACL2 ENSG00000261846    344752
## 11525    ARHGEF26-AS1 ENSG00000281157 100507524
## 11527        ARHGEF26 ENSG00000277101     26084
## 11529           DHX36 ENSG00000281763    170506
## 11619          SCHIP1 ENSG00000283154     29970
## 11803         MIR4789 ENSG00000285406 100616395
## 12160           MUC20 ENSG00000275430    200958
## 12161           MUC20 ENSG00000277753    200958
## 12162           MUC20 ENSG00000278114    200958
## 12163           MUC20 ENSG00000281630    200958
## 12164           MUC20 ENSG00000274843    200958
## 12165           MUC20 ENSG00000275501    200958
## 12166           MUC20 ENSG00000276583    200958
## 12168            MUC4 ENSG00000276613      4585
## 12169            MUC4 ENSG00000278303      4585
## 12170            MUC4 ENSG00000273984      4585
## 12171            MUC4 ENSG00000273822      4585
## 12172            MUC4 ENSG00000278468      4585
## 12173            MUC4 ENSG00000275164      4585
## 12174            MUC4 ENSG00000277585      4585
## 12241            BDH1 ENSG00000275544       622
## 12261       ANKRD18DP ENSG00000281617    348840
## 12336          FAM53A ENSG00000288647    152877
## 12488            HMX1 ENSG00000288204      3166
## 12665          KCNIP4 ENSG00000281758     80333
## 12942             TEC            <NA> 100124696
## 13184          YTHDC1 ENSG00000275272     91746
## 13187       TMPRSS11E ENSG00000274058     28983
## 13194         UGT2B15 ENSG00000277132      7366
## 13199         UGT2B10 ENSG00000275190      7365
## 13209          UGT2A3 ENSG00000278216     79799
## 13247            CSN2 ENSG00000283030      1447
## 13249           STATH ENSG00000282891      6779
## 13251            HTN3 ENSG00000282967      3347
## 13253            HTN1 ENSG00000283046      3346
## 13255        CSN1S2AP ENSG00000283090    286828
## 13511         C4orf36 ENSG00000285458    132989
## 13554           HERC3 ENSG00000287542      8916
## 13888        CEP170P1 ENSG00000143702    645455
## 14310           DCHS2 ENSG00000284227     54798
## 14350           ASIC5 ENSG00000262505     51802
## 14352            TDO2 ENSG00000262635      6999
## 14354            CTSO ENSG00000263238      1519
## 14728       LINC01060 ENSG00000281580    401164
## 14746            FRG1 ENSG00000275145      2483
## 14747            FRG1 ENSG00000283153      2483
## 14748            FRG1 ENSG00000283630      2483
## 14756            FRG2 ENSG00000274972    448831
## 14757            FRG2 ENSG00000285063    448831
## 14758            FRG2 ENSG00000285202    448831
## 14770            DUX4 ENSG00000283949 100288687
## 14792          SLC9A3 ENSG00000281861      6550
## 14797           CEP72 ENSG00000280688     55722
## 14814            NKD2 ENSG00000276920     85409
## 14816         SLC12A7 ENSG00000276482     10723
## 14824         CLPTM1L ENSG00000274811     81037
## 14828          SLC6A3 ENSG00000276996      6531
## 14830          LPCAT1 ENSG00000275079     79888
## 15219        ADAMTS12 ENSG00000281690     81792
## 15222           RXFP3 ENSG00000277069     51289
## 15224         SLC45A2 ENSG00000281919     51151
## 15668          MRPS36 ENSG00000278461     92259
## 15670            CDK7 ENSG00000277273      1022
## 15672         CCDC125 ENSG00000277868    202243
## 15677            TAF9 ENSG00000276463      6880
## 15679           RAD17 ENSG00000276618      5884
## 15681        MARVELD2 ENSG00000274671    153562
## 15687            OCLN ENSG00000273814 100506658
## 15691         GTF2H2C ENSG00000276910    728340
## 15692         GTF2H2C ENSG00000275045    728340
## 15693         GTF2H2C ENSG00000145736    728340
## 15701          SERF1B ENSG00000277429    728492
## 15702          SERF1B ENSG00000278839    728492
## 15704            SMN2 ENSG00000273772      6607
## 15705            SMN2 ENSG00000277773      6607
## 15725          SERF1A ENSG00000277429      8293
## 15726          SERF1A ENSG00000275581      8293
## 15727          SERF1A ENSG00000278839      8293
## 15728          SERF1A ENSG00000205572      8293
## 15730            SMN1 ENSG00000273772      6606
## 15731            SMN1 ENSG00000275349      6606
## 15732            SMN1 ENSG00000277773      6606
## 15733            SMN1 ENSG00000205571      6606
## 15735            NAIP ENSG00000276068      4671
## 15736            NAIP ENSG00000278613      4671
## 15739          GTF2H2 ENSG00000276910      2966
## 15740          GTF2H2 ENSG00000275045      2966
## 15751          PMCHL2 ENSG00000280840      5370
## 15752          PMCHL2 ENSG00000275396      5370
## 15756            BDP1 ENSG00000274803     55814
## 15757            BDP1 ENSG00000273873     55814
## 15761           MCCC2 ENSG00000281742     64087
## 15762           MCCC2 ENSG00000275300     64087
## 15887           PDE8B ENSG00000284762      8622
## 16753           MATR3 ENSG00000280987      9782
## 16764         DNAJC18 ENSG00000288275    202052
## 16767           ECSCR ENSG00000288297    641700
## 16949           RBM27 ENSG00000275740     54439
## 17394         FAM153B ENSG00000251623    202134
## 17467           PROP1 ENSG00000274382      5626
## 17468           PROP1 ENSG00000280635      5626
## 17502         ADAMTS2 ENSG00000283802      9509
## 17512           RUFY1 ENSG00000284260     80230
## 17516         HNRNPH1 ENSG00000284254      3187
## 17521            CBY3 ENSG00000283718    646019
## 17523            CANX ENSG00000283777       821
## 17526           MAML1 ENSG00000283780      9794
## 17528           LTC4S ENSG00000283887      4056
## 17530          MGAT4B ENSG00000284501     11282
## 17532         MIR1229 ENSG00000283912 100302156
## 17534          SQSTM1 ENSG00000284099      8878
## 17539         TBC1D9B ENSG00000284400     23061
## 17676          FAM50B ENSG00000238158     26240
## 17782           GCNT2 ENSG00000285222      2651
## 17788         C6orf52 ENSG00000285312    347744
## 17790         PAK1IP1 ENSG00000285226     55003
## 17792         TMEM14C ENSG00000284936     51522
## 18155            GPX6 ENSG00000281185    257202
## 18157            GPX5 ENSG00000257770      2880
## 18163       LINC00533 ENSG00000249032    387055
## 18173           HCG14 ENSG00000234411    414760
## 18174           HCG14 ENSG00000237010    414760
## 18175           HCG14 ENSG00000227559    414760
## 18176           HCG14 ENSG00000236835    414760
## 18177           HCG14 ENSG00000230004    414760
## 18179          TRIM27 ENSG00000234495      5987
## 18180          TRIM27 ENSG00000229006      5987
## 18181          TRIM27 ENSG00000215641      5987
## 18182          TRIM27 ENSG00000233948      5987
## 18183          TRIM27 ENSG00000237462      5987
## 18184          TRIM27 ENSG00000237071      5987
## 18192          ZNF311 ENSG00000225351    282890
## 18193          ZNF311 ENSG00000223687    282890
## 18194          ZNF311 ENSG00000233831    282890
## 18195          ZNF311 ENSG00000235589    282890
## 18196          ZNF311 ENSG00000235178    282890
## 18197          ZNF311 ENSG00000169260    282890
## 18200           OR2W1 ENSG00000226463     26692
## 18201           OR2W1 ENSG00000228652     26692
## 18202           OR2W1 ENSG00000234101     26692
## 18203           OR2W1 ENSG00000227639     26692
## 18204           OR2W1 ENSG00000229328     26692
## 18205           OR2W1 ENSG00000228977     26692
## 18206           OR2W1 ENSG00000206525     26692
## 18210           OR2B3 ENSG00000233054    442184
## 18211           OR2B3 ENSG00000226832    442184
## 18212           OR2B3 ENSG00000231319    442184
## 18213           OR2B3 ENSG00000233687    442184
## 18214           OR2B3 ENSG00000233180    442184
## 18215           OR2B3 ENSG00000225736    442184
## 18216           OR2B3 ENSG00000206524    442184
## 18218           OR2J1 ENSG00000234305    442185
## 18219           OR2J1 ENSG00000206523    442185
## 18220           OR2J1 ENSG00000235632    442185
## 18221           OR2J1 ENSG00000225441    442185
## 18222           OR2J1 ENSG00000226931    442185
## 18223           OR2J1 ENSG00000226192    442185
## 18224           OR2J1 ENSG00000234804    442185
## 18226           OR2J3 ENSG00000226271    442186
## 18227           OR2J3 ENSG00000233636    442186
## 18228           OR2J3 ENSG00000232178    442186
## 18229           OR2J3 ENSG00000233618    442186
## 18230           OR2J3 ENSG00000230855    442186
## 18231           OR2J3 ENSG00000206522    442186
## 18232           OR2J3 ENSG00000229866    442186
## 18236           OR2J2 ENSG00000225550     26707
## 18237           OR2J2 ENSG00000226347     26707
## 18238           OR2J2 ENSG00000196231     26707
## 18239           OR2J2 ENSG00000226000     26707
## 18240           OR2J2 ENSG00000232945     26707
## 18241           OR2J2 ENSG00000234746     26707
## 18242           OR2J2 ENSG00000231676     26707
## 18251          OR14J1 ENSG00000236927    442191
## 18252          OR14J1 ENSG00000234100    442191
## 18253          OR14J1 ENSG00000112459    442191
## 18254          OR14J1 ENSG00000234195    442191
## 18255          OR14J1 ENSG00000237777    442191
## 18256          OR14J1 ENSG00000225291    442191
## 18259           OR5V1 ENSG00000242289     81696
## 18260           OR5V1 ENSG00000243441     81696
## 18261           OR5V1 ENSG00000233046     81696
## 18262           OR5V1 ENSG00000227137     81696
## 18263           OR5V1 ENSG00000230742     81696
## 18264           OR5V1 ENSG00000112461     81696
## 18265           OR5V1 ENSG00000240130     81696
## 18267          OR12D3 ENSG00000242022     81797
## 18268          OR12D3 ENSG00000204692     81797
## 18269          OR12D3 ENSG00000251394     81797
## 18270          OR12D3 ENSG00000229181     81797
## 18271          OR12D3 ENSG00000224487     81797
## 18272          OR12D3 ENSG00000250364     81797
## 18274          OR12D2 ENSG00000235966     26529
## 18275          OR12D2 ENSG00000204690     26529
## 18276          OR12D2 ENSG00000227446     26529
## 18277          OR12D2 ENSG00000233481     26529
## 18278          OR12D2 ENSG00000225247     26529
## 18280          OR12D1 ENSG00000249571     26530
## 18281          OR12D1 ENSG00000251547     26530
## 18282          OR12D1 ENSG00000248182     26530
## 18283          OR12D1 ENSG00000250294     26530
## 18284          OR12D1 ENSG00000249030     26530
## 18285          OR12D1 ENSG00000251608     26530
## 18287          OR11A1 ENSG00000232289     26531
## 18288          OR11A1 ENSG00000237258     26531
## 18289          OR11A1 ENSG00000223898     26531
## 18290          OR11A1 ENSG00000230780     26531
## 18291          OR11A1 ENSG00000206517     26531
## 18292          OR11A1 ENSG00000206472     26531
## 18293          OR11A1 ENSG00000234347     26531
## 18295          OR10C1 ENSG00000230505    442194
## 18296          OR10C1 ENSG00000235441    442194
## 18297          OR10C1 ENSG00000232397    442194
## 18298          OR10C1 ENSG00000229412    442194
## 18299          OR10C1 ENSG00000220550    442194
## 18300          OR10C1 ENSG00000224234    442194
## 18301          OR10C1 ENSG00000204689    442194
## 18303           OR2H1 ENSG00000229125     26716
## 18304           OR2H1 ENSG00000206471     26716
## 18305           OR2H1 ENSG00000224395     26716
## 18306           OR2H1 ENSG00000232984     26716
## 18307           OR2H1 ENSG00000206516     26716
## 18308           OR2H1 ENSG00000229408     26716
## 18309           OR2H1 ENSG00000235132     26716
## 18313           MAS1L ENSG00000206470    116511
## 18314           MAS1L ENSG00000234954    116511
## 18315           MAS1L ENSG00000237284    116511
## 18316           MAS1L ENSG00000228515    116511
## 18317           MAS1L ENSG00000228377    116511
## 18318           MAS1L ENSG00000233141    116511
## 18319           MAS1L ENSG00000206515    116511
## 18323       LINC01015 ENSG00000235788 100507362
## 18324       LINC01015 ENSG00000224446 100507362
## 18325       LINC01015 ENSG00000229383 100507362
## 18326       LINC01015 ENSG00000230674 100507362
## 18327       LINC01015 ENSG00000225426 100507362
## 18328       LINC01015 ENSG00000233857 100507362
## 18329       LINC01015 ENSG00000226687 100507362
## 18333             UBD ENSG00000226898     10537
## 18334             UBD ENSG00000228913     10537
## 18335             UBD ENSG00000224654     10537
## 18336             UBD ENSG00000206513     10537
## 18337             UBD ENSG00000231968     10537
## 18338             UBD ENSG00000206468     10537
## 18340          GABBR1 ENSG00000232569      2550
## 18341          GABBR1 ENSG00000237051      2550
## 18342          GABBR1 ENSG00000232632      2550
## 18343          GABBR1 ENSG00000206511      2550
## 18344          GABBR1 ENSG00000237112      2550
## 18345          GABBR1 ENSG00000206466      2550
## 18349        SNORD32B ENSG00000265634    692092
## 18350        SNORD32B ENSG00000265663    692092
## 18351        SNORD32B ENSG00000265926    692092
## 18352        SNORD32B ENSG00000265013    692092
## 18353        SNORD32B ENSG00000266672    692092
## 18354        SNORD32B ENSG00000266132    692092
## 18357           OR2H2 ENSG00000224319      7932
## 18358           OR2H2 ENSG00000206467      7932
## 18359           OR2H2 ENSG00000227044      7932
## 18360           OR2H2 ENSG00000229680      7932
## 18361           OR2H2 ENSG00000229185      7932
## 18362           OR2H2 ENSG00000206512      7932
## 18365             MOG ENSG00000234096      4340
## 18366             MOG ENSG00000230885      4340
## 18367             MOG ENSG00000234623      4340
## 18368             MOG ENSG00000137345      4340
## 18369             MOG ENSG00000236561      4340
## 18370             MOG ENSG00000232641      4340
## 18371             MOG ENSG00000237834      4340
## 18373           ZFP57 ENSG00000227858    346171
## 18374           ZFP57 ENSG00000223852    346171
## 18375           ZFP57 ENSG00000226858    346171
## 18376           ZFP57 ENSG00000234669    346171
## 18377           ZFP57 ENSG00000223858    346171
## 18378           ZFP57 ENSG00000232099    346171
## 18379           ZFP57 ENSG00000206510    346171
## 18382           HLA-F ENSG00000237508      3134
## 18383           HLA-F ENSG00000234487      3134
## 18384           HLA-F ENSG00000235220      3134
## 18385           HLA-F ENSG00000229698      3134
## 18386           HLA-F ENSG00000206509      3134
## 18387           HLA-F ENSG00000137403      3134
## 18390       HLA-F-AS1 ENSG00000206446    285830
## 18391       HLA-F-AS1 ENSG00000230545    285830
## 18392       HLA-F-AS1 ENSG00000226378    285830
## 18393       HLA-F-AS1 ENSG00000206508    285830
## 18394       HLA-F-AS1 ENSG00000230017    285830
## 18402           HLA-V ENSG00000224736    352962
## 18403           HLA-V ENSG00000206507    352962
## 18404           HLA-V ENSG00000229529    352962
## 18405           HLA-V ENSG00000223606    352962
## 18406           HLA-V ENSG00000229194    352962
## 18407           HLA-V ENSG00000206444    352962
## 18408           HLA-V ENSG00000230238    352962
## 18414           HLA-G ENSG00000276051      3135
## 18415           HLA-G ENSG00000233095      3135
## 18416           HLA-G ENSG00000235680      3135
## 18417           HLA-G ENSG00000230413      3135
## 18418           HLA-G ENSG00000235346      3135
## 18419           HLA-G ENSG00000237216      3135
## 18420           HLA-G ENSG00000206506      3135
## 18432           HLA-A ENSG00000227715      3105
## 18433           HLA-A ENSG00000229215      3105
## 18434           HLA-A ENSG00000223980      3105
## 18435           HLA-A ENSG00000206505      3105
## 18436           HLA-A ENSG00000224320      3105
## 18437           HLA-A ENSG00000231834      3105
## 18438           HLA-A ENSG00000235657      3105
## 18443            HCG9 ENSG00000234313     10255
## 18444            HCG9 ENSG00000237812     10255
## 18445            HCG9 ENSG00000236579     10255
## 18446            HCG9 ENSG00000227647     10255
## 18447            HCG9 ENSG00000206504     10255
## 18448            HCG9 ENSG00000234599     10255
## 18457         PPP1R11 ENSG00000233314      6992
## 18458         PPP1R11 ENSG00000236560      6992
## 18459         PPP1R11 ENSG00000237403      6992
## 18460         PPP1R11 ENSG00000234058      6992
## 18461         PPP1R11 ENSG00000206501      6992
## 18462         PPP1R11 ENSG00000227720      6992
## 18463         PPP1R11 ENSG00000237829      6992
## 18465           RNF39 ENSG00000236967     80352
## 18466           RNF39 ENSG00000230332     80352
## 18467           RNF39 ENSG00000206500     80352
## 18468           RNF39 ENSG00000235022     80352
## 18469           RNF39 ENSG00000227171     80352
## 18470           RNF39 ENSG00000230467     80352
## 18471           RNF39 ENSG00000237733     80352
## 18474          TRIM31 ENSG00000224542     11074
## 18475          TRIM31 ENSG00000224168     11074
## 18476          TRIM31 ENSG00000225130     11074
## 18477          TRIM31 ENSG00000137397     11074
## 18478          TRIM31 ENSG00000233573     11074
## 18479          TRIM31 ENSG00000223531     11074
## 18480          TRIM31 ENSG00000226402     11074
## 18482      TRIM31-AS1 ENSG00000235722 104533120
## 18483      TRIM31-AS1 ENSG00000237050 104533120
## 18484      TRIM31-AS1 ENSG00000232510 104533120
## 18485      TRIM31-AS1 ENSG00000225732 104533120
## 18486      TRIM31-AS1 ENSG00000229223 104533120
## 18487      TRIM31-AS1 ENSG00000225038 104533120
## 18488      TRIM31-AS1 ENSG00000238027 104533120
## 18490          TRIM40 ENSG00000224496    135644
## 18491          TRIM40 ENSG00000236399    135644
## 18492          TRIM40 ENSG00000172524    135644
## 18493          TRIM40 ENSG00000237046    135644
## 18494          TRIM40 ENSG00000228001    135644
## 18495          TRIM40 ENSG00000227458    135644
## 18496          TRIM40 ENSG00000233931    135644
## 18498          TRIM10 ENSG00000237703     10107
## 18499          TRIM10 ENSG00000229346     10107
## 18500          TRIM10 ENSG00000137394     10107
## 18501          TRIM10 ENSG00000235025     10107
## 18502          TRIM10 ENSG00000227472     10107
## 18503          TRIM10 ENSG00000237192     10107
## 18504          TRIM10 ENSG00000229381     10107
## 18506          TRIM15 ENSG00000235259     89870
## 18507          TRIM15 ENSG00000235960     89870
## 18508          TRIM15 ENSG00000137384     89870
## 18509          TRIM15 ENSG00000224145     89870
## 18510          TRIM15 ENSG00000227147     89870
## 18511          TRIM15 ENSG00000233599     89870
## 18512          TRIM15 ENSG00000235905     89870
## 18514          TRIM26 ENSG00000231002      7726
## 18515          TRIM26 ENSG00000228881      7726
## 18516          TRIM26 ENSG00000226060      7726
## 18517          TRIM26 ENSG00000234046      7726
## 18518          TRIM26 ENSG00000230230      7726
## 18519          TRIM26 ENSG00000137313      7726
## 18520          TRIM26 ENSG00000231641      7726
## 18523           HCG17 ENSG00000236729    414778
## 18524           HCG17 ENSG00000241701    414778
## 18525           HCG17 ENSG00000240924    414778
## 18526           HCG17 ENSG00000241053    414778
## 18527           HCG17 ENSG00000244695    414778
## 18528           HCG17 ENSG00000240833    414778
## 18531           HLA-L ENSG00000242227      3139
## 18532           HLA-L ENSG00000241166      3139
## 18533           HLA-L ENSG00000239618      3139
## 18534           HLA-L ENSG00000243492      3139
## 18535           HLA-L ENSG00000244721      3139
## 18537           HCG18 ENSG00000235727    414777
## 18538           HCG18 ENSG00000228894    414777
## 18539           HCG18 ENSG00000234893    414777
## 18540           HCG18 ENSG00000230660    414777
## 18541           HCG18 ENSG00000224705    414777
## 18542           HCG18 ENSG00000224619    414777
## 18544          TRIM39 ENSG00000226437     56658
## 18545          TRIM39 ENSG00000224994     56658
## 18546          TRIM39 ENSG00000232839     56658
## 18547          TRIM39 ENSG00000206495     56658
## 18548          TRIM39 ENSG00000230308     56658
## 18549          TRIM39 ENSG00000229929     56658
## 18551    TRIM39-RPP21 ENSG00000241779    202658
## 18552    TRIM39-RPP21 ENSG00000239927    202658
## 18553    TRIM39-RPP21 ENSG00000241863    202658
## 18554    TRIM39-RPP21 ENSG00000243009    202658
## 18555    TRIM39-RPP21 ENSG00000242726    202658
## 18556    TRIM39-RPP21 ENSG00000239865    202658
## 18557    TRIM39-RPP21 ENSG00000241370    202658
## 18559           RPP21 ENSG00000241779     79897
## 18560           RPP21 ENSG00000239927     79897
## 18561           RPP21 ENSG00000241863     79897
## 18562           RPP21 ENSG00000243009     79897
## 18563           RPP21 ENSG00000242726     79897
## 18564           RPP21 ENSG00000239865     79897
## 18573           HLA-E ENSG00000206493      3133
## 18574           HLA-E ENSG00000236632      3133
## 18575           HLA-E ENSG00000225201      3133
## 18576           HLA-E ENSG00000230254      3133
## 18577           HLA-E ENSG00000229252      3133
## 18578           HLA-E ENSG00000233904      3133
## 18581            GNL1 ENSG00000229470      2794
## 18582            GNL1 ENSG00000206412      2794
## 18583            GNL1 ENSG00000235986      2794
## 18584            GNL1 ENSG00000226882      2794
## 18585            GNL1 ENSG00000228581      2794
## 18586            GNL1 ENSG00000232143      2794
## 18587            GNL1 ENSG00000206492      2794
## 18589            PRR3 ENSG00000223887     80742
## 18590            PRR3 ENSG00000223766     80742
## 18591            PRR3 ENSG00000228186     80742
## 18592            PRR3 ENSG00000233564     80742
## 18593            PRR3 ENSG00000229202     80742
## 18594            PRR3 ENSG00000206491     80742
## 18596           ABCF1 ENSG00000225989        23
## 18597           ABCF1 ENSG00000236149        23
## 18598           ABCF1 ENSG00000232169        23
## 18599           ABCF1 ENSG00000231129        23
## 18600           ABCF1 ENSG00000236342        23
## 18601           ABCF1 ENSG00000206490        23
## 18604         PPP1R10 ENSG00000230995      5514
## 18605         PPP1R10 ENSG00000231737      5514
## 18606         PPP1R10 ENSG00000238104      5514
## 18607         PPP1R10 ENSG00000235291      5514
## 18608         PPP1R10 ENSG00000206489      5514
## 18609         PPP1R10 ENSG00000227804      5514
## 18612         MRPS18B ENSG00000233813     28973
## 18613         MRPS18B ENSG00000229861     28973
## 18614         MRPS18B ENSG00000227420     28973
## 18615         MRPS18B ENSG00000203624     28973
## 18616         MRPS18B ENSG00000226111     28973
## 18617         MRPS18B ENSG00000223775     28973
## 18619           ATAT1 ENSG00000234549     79969
## 18620           ATAT1 ENSG00000231257     79969
## 18621           ATAT1 ENSG00000206488     79969
## 18622           ATAT1 ENSG00000229061     79969
## 18623           ATAT1 ENSG00000235658     79969
## 18624           ATAT1 ENSG00000223752     79969
## 18627        C6orf136 ENSG00000224120    221545
## 18628        C6orf136 ENSG00000233164    221545
## 18629        C6orf136 ENSG00000233641    221545
## 18630        C6orf136 ENSG00000237100    221545
## 18631        C6orf136 ENSG00000237012    221545
## 18632        C6orf136 ENSG00000206487    221545
## 18635           DHX16 ENSG00000227222      8449
## 18636           DHX16 ENSG00000226171      8449
## 18637           DHX16 ENSG00000233049      8449
## 18638           DHX16 ENSG00000233418      8449
## 18639           DHX16 ENSG00000233561      8449
## 18640           DHX16 ENSG00000206486      8449
## 18641           DHX16 ENSG00000231377      8449
## 18643         PPP1R18 ENSG00000230341    170954
## 18644         PPP1R18 ENSG00000236428    170954
## 18645         PPP1R18 ENSG00000229998    170954
## 18646         PPP1R18 ENSG00000225060    170954
## 18647         PPP1R18 ENSG00000234000    170954
## 18648         PPP1R18 ENSG00000231247    170954
## 18649         PPP1R18 ENSG00000206485    170954
## 18651             NRM ENSG00000236843     11270
## 18652             NRM ENSG00000228854     11270
## 18653             NRM ENSG00000228867     11270
## 18654             NRM ENSG00000234809     11270
## 18655             NRM ENSG00000235773     11270
## 18656             NRM ENSG00000206484     11270
## 18659            MDC1 ENSG00000234012      9656
## 18660            MDC1 ENSG00000225589      9656
## 18661            MDC1 ENSG00000224587      9656
## 18662            MDC1 ENSG00000237095      9656
## 18663            MDC1 ENSG00000228575      9656
## 18664            MDC1 ENSG00000206481      9656
## 18665            MDC1 ENSG00000231135      9656
## 18667        MDC1-AS1 ENSG00000236522 106478956
## 18668        MDC1-AS1 ENSG00000231860 106478956
## 18669        MDC1-AS1 ENSG00000229681 106478956
## 18670        MDC1-AS1 ENSG00000224508 106478956
## 18671        MDC1-AS1 ENSG00000227899 106478956
## 18672        MDC1-AS1 ENSG00000233883 106478956
## 18673        MDC1-AS1 ENSG00000236766 106478956
## 18675            TUBB ENSG00000224156    203068
## 18676            TUBB ENSG00000235067    203068
## 18677            TUBB ENSG00000229684    203068
## 18678            TUBB ENSG00000232575    203068
## 18679            TUBB ENSG00000232421    203068
## 18680            TUBB ENSG00000183311    203068
## 18681            TUBB ENSG00000227739    203068
## 18684           FLOT1 ENSG00000223654     10211
## 18685           FLOT1 ENSG00000236271     10211
## 18686           FLOT1 ENSG00000206480     10211
## 18687           FLOT1 ENSG00000232280     10211
## 18688           FLOT1 ENSG00000206379     10211
## 18689           FLOT1 ENSG00000230143     10211
## 18690           FLOT1 ENSG00000224740     10211
## 18693            IER3 ENSG00000235030      8870
## 18694            IER3 ENSG00000230128      8870
## 18695            IER3 ENSG00000237155      8870
## 18696            IER3 ENSG00000227231      8870
## 18697            IER3 ENSG00000206478      8870
## 18700           HCG20 ENSG00000224923 105375013
## 18701           HCG20 ENSG00000238216 105375013
## 18702           HCG20 ENSG00000228762 105375013
## 18703           HCG20 ENSG00000224641 105375013
## 18704           HCG20 ENSG00000224133 105375013
## 18706       LINC00243 ENSG00000227596    401247
## 18707       LINC00243 ENSG00000237890    401247
## 18708       LINC00243 ENSG00000236006    401247
## 18709       LINC00243 ENSG00000215523    401247
## 18710       LINC00243 ENSG00000229170    401247
## 18715            DDR1 ENSG00000223680       780
## 18716            DDR1 ENSG00000229767       780
## 18717            DDR1 ENSG00000234078       780
## 18718            DDR1 ENSG00000215522       780
## 18719            DDR1 ENSG00000230456       780
## 18720            DDR1 ENSG00000137332       780
## 18724          GTF2H4 ENSG00000226384      2968
## 18725          GTF2H4 ENSG00000234370      2968
## 18726          GTF2H4 ENSG00000233149      2968
## 18727          GTF2H4 ENSG00000236895      2968
## 18728          GTF2H4 ENSG00000221974      2968
## 18730           VARS2 ENSG00000223494     57176
## 18731           VARS2 ENSG00000236178     57176
## 18732           VARS2 ENSG00000230985     57176
## 18733           VARS2 ENSG00000234032     57176
## 18734           VARS2 ENSG00000206476     57176
## 18736           SFTA2 ENSG00000237814    389376
## 18737           SFTA2 ENSG00000225454    389376
## 18738           SFTA2 ENSG00000230072    389376
## 18739           SFTA2 ENSG00000206465    389376
## 18740           SFTA2 ENSG00000224246    389376
## 18744           MUC21 ENSG00000231350    394263
## 18745           MUC21 ENSG00000223590    394263
## 18746           MUC21 ENSG00000234137    394263
## 18747           MUC21 ENSG00000227506    394263
## 18748           MUC21 ENSG00000237962    394263
## 18749           MUC21 ENSG00000206463    394263
## 18752           HCG22 ENSG00000228147    285834
## 18753           HCG22 ENSG00000238234    285834
## 18754           HCG22 ENSG00000237894    285834
## 18755           HCG22 ENSG00000227974    285834
## 18756           HCG22 ENSG00000229501    285834
## 18757           HCG22 ENSG00000237093    285834
## 18758           HCG22 ENSG00000225629    285834
## 18761         C6orf15 ENSG00000231624     29113
## 18762         C6orf15 ENSG00000206461     29113
## 18763         C6orf15 ENSG00000224105     29113
## 18764         C6orf15 ENSG00000225543     29113
## 18765         C6orf15 ENSG00000229432     29113
## 18767        PSORS1C1 ENSG00000231094    170679
## 18768        PSORS1C1 ENSG00000235487    170679
## 18769        PSORS1C1 ENSG00000233439    170679
## 18770        PSORS1C1 ENSG00000233734    170679
## 18771        PSORS1C1 ENSG00000206458    170679
## 18773            CDSN ENSG00000237123      1041
## 18774            CDSN ENSG00000237165      1041
## 18775            CDSN ENSG00000206460      1041
## 18776            CDSN ENSG00000237114      1041
## 18777            CDSN ENSG00000137197      1041
## 18779        PSORS1C2 ENSG00000224544    170680
## 18780        PSORS1C2 ENSG00000232127    170680
## 18781        PSORS1C2 ENSG00000227246    170680
## 18782        PSORS1C2 ENSG00000234605    170680
## 18783        PSORS1C2 ENSG00000206459    170680
## 18786          CCHCR1 ENSG00000206355     54535
## 18787          CCHCR1 ENSG00000234114     54535
## 18788          CCHCR1 ENSG00000223533     54535
## 18789          CCHCR1 ENSG00000224180     54535
## 18790          CCHCR1 ENSG00000206457     54535
## 18792           TCF19 ENSG00000224472      6941
## 18793           TCF19 ENSG00000224941      6941
## 18794           TCF19 ENSG00000206455      6941
## 18795           TCF19 ENSG00000233890      6941
## 18796           TCF19 ENSG00000224379      6941
## 18797           TCF19 ENSG00000234674      6941
## 18799          POU5F1 ENSG00000233911      5460
## 18800          POU5F1 ENSG00000206454      5460
## 18801          POU5F1 ENSG00000230336      5460
## 18802          POU5F1 ENSG00000237582      5460
## 18803          POU5F1 ENSG00000229094      5460
## 18804          POU5F1 ENSG00000235068      5460
## 18808           HCG27 ENSG00000234079    253018
## 18809           HCG27 ENSG00000238148    253018
## 18810           HCG27 ENSG00000231281    253018
## 18811           HCG27 ENSG00000232758    253018
## 18812           HCG27 ENSG00000220890    253018
## 18813           HCG27 ENSG00000223577    253018
## 18818           HLA-C ENSG00000206435      3107
## 18819           HLA-C ENSG00000233841      3107
## 18820           HLA-C ENSG00000237022      3107
## 18821           HLA-C ENSG00000206452      3107
## 18822           HLA-C ENSG00000228299      3107
## 18823           HLA-C ENSG00000225691      3107
## 18830           HLA-B ENSG00000206450      3106
## 18831           HLA-B ENSG00000228964      3106
## 18832           HLA-B ENSG00000223532      3106
## 18833           HLA-B ENSG00000224608      3106
## 18834           HLA-B ENSG00000232126      3106
## 18844            HCP5 ENSG00000237105     10866
## 18845            HCP5 ENSG00000227429     10866
## 18846            HCP5 ENSG00000230389     10866
## 18848            MICA ENSG00000233051 100507436
## 18849            MICA ENSG00000231225 100507436
## 18850            MICA ENSG00000235233 100507436
## 18851            MICA ENSG00000183214 100507436
## 18855            MICB ENSG00000231179      4277
## 18856            MICB ENSG00000238289      4277
## 18857            MICB ENSG00000234218      4277
## 18858            MICB ENSG00000224378      4277
## 18859            MICB ENSG00000227772      4277
## 18860            MICB ENSG00000231372      4277
## 18861            MICB ENSG00000206449      4277
## 18866           MCCD1 ENSG00000225228    401250
## 18867           MCCD1 ENSG00000228662    401250
## 18868           MCCD1 ENSG00000238238    401250
## 18869           MCCD1 ENSG00000226841    401250
## 18870           MCCD1 ENSG00000231975    401250
## 18871           MCCD1 ENSG00000206447    401250
## 18872           MCCD1 ENSG00000226923    401250
## 18875          DDX39B ENSG00000237889      7919
## 18876          DDX39B ENSG00000225859      7919
## 18877          DDX39B ENSG00000235439      7919
## 18878          DDX39B ENSG00000225073      7919
## 18879          DDX39B ENSG00000230624      7919
## 18880          DDX39B ENSG00000229496      7919
## 18881          DDX39B ENSG00000215425      7919
## 18883        SNORD117 ENSG00000265849    692233
## 18884        SNORD117 ENSG00000265116    692233
## 18885        SNORD117 ENSG00000263358    692233
## 18886        SNORD117 ENSG00000266419    692233
## 18887        SNORD117 ENSG00000263625    692233
## 18888        SNORD117 ENSG00000263359    692233
## 18889        SNORD117 ENSG00000266295    692233
## 18891         SNORD84 ENSG00000265325    692199
## 18892         SNORD84 ENSG00000263442    692199
## 18893         SNORD84 ENSG00000264591    692199
## 18894         SNORD84 ENSG00000266755    692199
## 18895         SNORD84 ENSG00000265607    692199
## 18896         SNORD84 ENSG00000266646    692199
## 18898      DDX39B-AS1 ENSG00000234082 106478957
## 18899      DDX39B-AS1 ENSG00000231647 106478957
## 18900      DDX39B-AS1 ENSG00000236019 106478957
## 18901      DDX39B-AS1 ENSG00000238071 106478957
## 18902      DDX39B-AS1 ENSG00000228245 106478957
## 18903      DDX39B-AS1 ENSG00000232256 106478957
## 18905        ATP6V1G2 ENSG00000234920       534
## 18906        ATP6V1G2 ENSG00000226850       534
## 18907        ATP6V1G2 ENSG00000234668       534
## 18908        ATP6V1G2 ENSG00000230900       534
## 18909        ATP6V1G2 ENSG00000206445       534
## 18910        ATP6V1G2 ENSG00000227587       534
## 18912         NFKBIL1 ENSG00000236346      4795
## 18913         NFKBIL1 ENSG00000236196      4795
## 18914         NFKBIL1 ENSG00000206440      4795
## 18915         NFKBIL1 ENSG00000227565      4795
## 18916         NFKBIL1 ENSG00000235125      4795
## 18917         NFKBIL1 ENSG00000234530      4795
## 18919             LTA ENSG00000230279      4049
## 18920             LTA ENSG00000238130      4049
## 18921             LTA ENSG00000231408      4049
## 18922             LTA ENSG00000223919      4049
## 18923             LTA ENSG00000173503      4049
## 18924             LTA ENSG00000226275      4049
## 18926             TNF ENSG00000228978      7124
## 18927             TNF ENSG00000204490      7124
## 18928             TNF ENSG00000223952      7124
## 18929             TNF ENSG00000228849      7124
## 18930             TNF ENSG00000228321      7124
## 18931             TNF ENSG00000230108      7124
## 18932             TNF ENSG00000206439      7124
## 18934             LTB ENSG00000223448      4050
## 18935             LTB ENSG00000231314      4050
## 18936             LTB ENSG00000204487      4050
## 18937             LTB ENSG00000236925      4050
## 18938             LTB ENSG00000238114      4050
## 18939             LTB ENSG00000236237      4050
## 18940             LTB ENSG00000206437      4050
## 18942            LST1 ENSG00000235915      7940
## 18943            LST1 ENSG00000230791      7940
## 18944            LST1 ENSG00000206433      7940
## 18945            LST1 ENSG00000231048      7940
## 18946            LST1 ENSG00000234514      7940
## 18947            LST1 ENSG00000223465      7940
## 18948            LST1 ENSG00000226182      7940
## 18950            NCR3 ENSG00000236315    259197
## 18951            NCR3 ENSG00000206430    259197
## 18952            NCR3 ENSG00000236979    259197
## 18953            NCR3 ENSG00000237808    259197
## 18954            NCR3 ENSG00000223833    259197
## 18955            NCR3 ENSG00000237103    259197
## 18956            NCR3 ENSG00000225211    259197
## 18959            AIF1 ENSG00000235588       199
## 18960            AIF1 ENSG00000234836       199
## 18961            AIF1 ENSG00000206428       199
## 18962            AIF1 ENSG00000235985       199
## 18963            AIF1 ENSG00000237727       199
## 18965          PRRC2A ENSG00000226618      7916
## 18966          PRRC2A ENSG00000231370      7916
## 18967          PRRC2A ENSG00000231825      7916
## 18968          PRRC2A ENSG00000225748      7916
## 18969          PRRC2A ENSG00000206427      7916
## 18970          PRRC2A ENSG00000225164      7916
## 18972         SNORA38 ENSG00000266847    677820
## 18973         SNORA38 ENSG00000263994    677820
## 18974         SNORA38 ENSG00000266004    677820
## 18975         SNORA38 ENSG00000265754    677820
## 18976         SNORA38 ENSG00000263879    677820
## 18977         SNORA38 ENSG00000264153    677820
## 18979            BAG6 ENSG00000228760      7917
## 18980            BAG6 ENSG00000229524      7917
## 18981            BAG6 ENSG00000234651      7917
## 18982            BAG6 ENSG00000096155      7917
## 18983            BAG6 ENSG00000227761      7917
## 18984            BAG6 ENSG00000233348      7917
## 18986            APOM ENSG00000235754     55937
## 18987            APOM ENSG00000206409     55937
## 18988            APOM ENSG00000231974     55937
## 18989            APOM ENSG00000224290     55937
## 18990            APOM ENSG00000226215     55937
## 18991            APOM ENSG00000227567     55937
## 18993         C6orf47 ENSG00000228177     57827
## 18994         C6orf47 ENSG00000226103     57827
## 18995         C6orf47 ENSG00000203623     57827
## 18996         C6orf47 ENSG00000226531     57827
## 18997         C6orf47 ENSG00000228435     57827
## 18998         C6orf47 ENSG00000235360     57827
## 19001          GPANK1 ENSG00000223932      7918
## 19002          GPANK1 ENSG00000233210      7918
## 19003          GPANK1 ENSG00000206408      7918
## 19004          GPANK1 ENSG00000228605      7918
## 19005          GPANK1 ENSG00000232312      7918
## 19006          GPANK1 ENSG00000236011      7918
## 19008          CSNK2B ENSG00000230700      1460
## 19009          CSNK2B ENSG00000232960      1460
## 19010          CSNK2B ENSG00000206406      1460
## 19011          CSNK2B ENSG00000224774      1460
## 19012          CSNK2B ENSG00000224398      1460
## 19013          CSNK2B ENSG00000228875      1460
## 19016          LY6G5B ENSG00000240433     58496
## 19017          LY6G5B ENSG00000239497     58496
## 19018          LY6G5B ENSG00000244672     58496
## 19019          LY6G5B ENSG00000241132     58496
## 19020          LY6G5B ENSG00000241713     58496
## 19021          LY6G5B ENSG00000239285     58496
## 19023          LY6G5C ENSG00000231325     80741
## 19024          LY6G5C ENSG00000237495     80741
## 19025          LY6G5C ENSG00000228883     80741
## 19026          LY6G5C ENSG00000226404     80741
## 19027          LY6G5C ENSG00000111971     80741
## 19028          LY6G5C ENSG00000206404     80741
## 19030         ABHD16A ENSG00000231488      7920
## 19031         ABHD16A ENSG00000224552      7920
## 19032         ABHD16A ENSG00000206403      7920
## 19033         ABHD16A ENSG00000236063      7920
## 19034         ABHD16A ENSG00000230475      7920
## 19035         ABHD16A ENSG00000235676      7920
## 19039          LY6G6F ENSG00000239741    259215
## 19040          LY6G6F ENSG00000240957    259215
## 19041          LY6G6F ENSG00000240008    259215
## 19042          LY6G6F ENSG00000241822    259215
## 19043          LY6G6F ENSG00000243003    259215
## 19044          LY6G6F ENSG00000243804    259215
## 19048          LY6G6D ENSG00000225993     58530
## 19049          LY6G6D ENSG00000235302     58530
## 19050          LY6G6D ENSG00000226603     58530
## 19051          LY6G6D ENSG00000206402     58530
## 19052          LY6G6D ENSG00000234443     58530
## 19053          LY6G6D ENSG00000236902     58530
## 19056          LY6G6C ENSG00000228859     80740
## 19057          LY6G6C ENSG00000235925     80740
## 19058          LY6G6C ENSG00000206398     80740
## 19059          LY6G6C ENSG00000235452     80740
## 19060          LY6G6C ENSG00000236183     80740
## 19061          LY6G6C ENSG00000228250     80740
## 19063           DDAH2 ENSG00000226634     23564
## 19064           DDAH2 ENSG00000225635     23564
## 19065           DDAH2 ENSG00000227317     23564
## 19066           DDAH2 ENSG00000206395     23564
## 19067           DDAH2 ENSG00000228128     23564
## 19068           DDAH2 ENSG00000233076     23564
## 19070           CLIC1 ENSG00000226651      1192
## 19071           CLIC1 ENSG00000230685      1192
## 19072           CLIC1 ENSG00000223639      1192
## 19073           CLIC1 ENSG00000226248      1192
## 19074           CLIC1 ENSG00000226417      1192
## 19075           CLIC1 ENSG00000206394      1192
## 19077            MSH5 ENSG00000233345      4439
## 19078            MSH5 ENSG00000230293      4439
## 19079            MSH5 ENSG00000227314      4439
## 19080            MSH5 ENSG00000235222      4439
## 19081            MSH5 ENSG00000230961      4439
## 19082            MSH5 ENSG00000237333      4439
## 19083            MSH5 ENSG00000235569      4439
## 19087          SAPCD1 ENSG00000227861    401251
## 19088          SAPCD1 ENSG00000234951    401251
## 19089          SAPCD1 ENSG00000237918    401251
## 19090          SAPCD1 ENSG00000227074    401251
## 19091          SAPCD1 ENSG00000229176    401251
## 19094            VWA7 ENSG00000223757     80737
## 19095            VWA7 ENSG00000238203     80737
## 19096            VWA7 ENSG00000234433     80737
## 19097            VWA7 ENSG00000227144     80737
## 19098            VWA7 ENSG00000230048     80737
## 19101            LSM2 ENSG00000224979     57819
## 19102            LSM2 ENSG00000236826     57819
## 19103            LSM2 ENSG00000172850     57819
## 19104            LSM2 ENSG00000231502     57819
## 19105            LSM2 ENSG00000225998     57819
## 19107          HSPA1L ENSG00000226704      3305
## 19108          HSPA1L ENSG00000236251      3305
## 19109          HSPA1L ENSG00000206383      3305
## 19110          HSPA1L ENSG00000234258      3305
## 19112          HSPA1A ENSG00000235941      3303
## 19113          HSPA1A ENSG00000237724      3303
## 19114          HSPA1A ENSG00000234475      3303
## 19115          HSPA1A ENSG00000215328      3303
## 19117          HSPA1B ENSG00000232804      3304
## 19118          HSPA1B ENSG00000231555      3304
## 19119          HSPA1B ENSG00000224501      3304
## 19120          HSPA1B ENSG00000212866      3304
## 19123         SNORD48 ENSG00000263864     26801
## 19124         SNORD48 ENSG00000264086     26801
## 19125         SNORD48 ENSG00000264202     26801
## 19126         SNORD48 ENSG00000265732     26801
## 19128         SNORD52 ENSG00000266300     26797
## 19129         SNORD52 ENSG00000265707     26797
## 19130         SNORD52 ENSG00000263362     26797
## 19131         SNORD52 ENSG00000265156     26797
## 19133            NEU1 ENSG00000228691      4758
## 19134            NEU1 ENSG00000234343      4758
## 19135            NEU1 ENSG00000184494      4758
## 19136            NEU1 ENSG00000227315      4758
## 19137            NEU1 ENSG00000223957      4758
## 19138            NEU1 ENSG00000234846      4758
## 19139            NEU1 ENSG00000227129      4758
## 19141         SLC44A4 ENSG00000235336     80736
## 19142         SLC44A4 ENSG00000203463     80736
## 19143         SLC44A4 ENSG00000232180     80736
## 19144         SLC44A4 ENSG00000229077     80736
## 19145         SLC44A4 ENSG00000228263     80736
## 19146         SLC44A4 ENSG00000231479     80736
## 19147         SLC44A4 ENSG00000206378     80736
## 19149           EHMT2 ENSG00000232045     10919
## 19150           EHMT2 ENSG00000238134     10919
## 19151           EHMT2 ENSG00000224143     10919
## 19152           EHMT2 ENSG00000227333     10919
## 19153           EHMT2 ENSG00000236759     10919
## 19154           EHMT2 ENSG00000206376     10919
## 19157              C2 ENSG00000231543       717
## 19158              C2 ENSG00000206372       717
## 19159              C2 ENSG00000204364       717
## 19160              C2 ENSG00000226560       717
## 19161              C2 ENSG00000235696       717
## 19162              C2 ENSG00000235017       717
## 19164          ZBTB12 ENSG00000206366    221527
## 19165          ZBTB12 ENSG00000234852    221527
## 19166          ZBTB12 ENSG00000234196    221527
## 19167          ZBTB12 ENSG00000237900    221527
## 19169             CFB ENSG00000242335       629
## 19170             CFB ENSG00000241534       629
## 19171             CFB ENSG00000204359       629
## 19172             CFB ENSG00000243570       629
## 19173             CFB ENSG00000241253       629
## 19174             CFB ENSG00000239754       629
## 19176           NELFE ENSG00000206268      7936
## 19177           NELFE ENSG00000233801      7936
## 19178           NELFE ENSG00000229363      7936
## 19179           NELFE ENSG00000206357      7936
## 19180           NELFE ENSG00000231044      7936
## 19183          SKIV2L ENSG00000223493      6499
## 19184          SKIV2L ENSG00000206353      6499
## 19185          SKIV2L ENSG00000232616      6499
## 19186          SKIV2L ENSG00000228896      6499
## 19187          SKIV2L ENSG00000225737      6499
## 19189             DXO ENSG00000224313      1797
## 19190             DXO ENSG00000225682      1797
## 19191             DXO ENSG00000206346      1797
## 19192             DXO ENSG00000236765      1797
## 19193             DXO ENSG00000234798      1797
## 19195           STK19 ENSG00000236250      8859
## 19196           STK19 ENSG00000226033      8859
## 19197           STK19 ENSG00000226257      8859
## 19198           STK19 ENSG00000206342      8859
## 19199           STK19 ENSG00000234947      8859
## 19201             C4A ENSG00000227746       720
## 19202             C4A ENSG00000244207       720
## 19203             C4A ENSG00000206340       720
## 19210             C4B ENSG00000224639       721
## 19211             C4B ENSG00000228454       721
## 19212             C4B ENSG00000236625       721
## 19213             C4B ENSG00000228267       721
## 19216         CYP21A2 ENSG00000232414      1589
## 19217         CYP21A2 ENSG00000198457      1589
## 19218         CYP21A2 ENSG00000233151      1589
## 19219         CYP21A2 ENSG00000235134      1589
## 19220         CYP21A2 ENSG00000206338      1589
## 19222            TNXB ENSG00000229341      7148
## 19223            TNXB ENSG00000236221      7148
## 19224            TNXB ENSG00000231608      7148
## 19225            TNXB ENSG00000229353      7148
## 19226            TNXB ENSG00000206258      7148
## 19227            TNXB ENSG00000236236      7148
## 19228            TNXB ENSG00000233323      7148
## 19231           ATF6B ENSG00000228628      1388
## 19232           ATF6B ENSG00000234539      1388
## 19233           ATF6B ENSG00000168468      1388
## 19235           FKBPL ENSG00000223666     63943
## 19236           FKBPL ENSG00000224200     63943
## 19237           FKBPL ENSG00000230907     63943
## 19239           PRRT1 ENSG00000238056     80863
## 19240           PRRT1 ENSG00000229071     80863
## 19241           PRRT1 ENSG00000225141     80863
## 19242           PRRT1 ENSG00000235956     80863
## 19243           PRRT1 ENSG00000229488     80863
## 19244           PRRT1 ENSG00000227122     80863
## 19245           PRRT1 ENSG00000206331     80863
## 19247            PPT2 ENSG00000168452      9374
## 19248            PPT2 ENSG00000206256      9374
## 19249            PPT2 ENSG00000227600      9374
## 19250            PPT2 ENSG00000236649      9374
## 19251            PPT2 ENSG00000228116      9374
## 19252            PPT2 ENSG00000206329      9374
## 19253            PPT2 ENSG00000231618      9374
## 19256           EGFL8 ENSG00000240389     80864
## 19257           EGFL8 ENSG00000239974     80864
## 19258           EGFL8 ENSG00000242038     80864
## 19259           EGFL8 ENSG00000240592     80864
## 19260           EGFL8 ENSG00000244444     80864
## 19261           EGFL8 ENSG00000243897     80864
## 19263          AGPAT1 ENSG00000236873     10554
## 19264          AGPAT1 ENSG00000226467     10554
## 19265          AGPAT1 ENSG00000227642     10554
## 19266          AGPAT1 ENSG00000206324     10554
## 19267          AGPAT1 ENSG00000235758     10554
## 19268          AGPAT1 ENSG00000228892     10554
## 19270            RNF5 ENSG00000223767      6048
## 19271            RNF5 ENSG00000228907      6048
## 19272            RNF5 ENSG00000227277      6048
## 19273            RNF5 ENSG00000225452      6048
## 19274            RNF5 ENSG00000183574      6048
## 19275            RNF5 ENSG00000228405      6048
## 19277            AGER ENSG00000231268       177
## 19278            AGER ENSG00000229058       177
## 19279            AGER ENSG00000230514       177
## 19280            AGER ENSG00000237405       177
## 19281            AGER ENSG00000206320       177
## 19282            AGER ENSG00000234729       177
## 19284            PBX2 ENSG00000225987      5089
## 19285            PBX2 ENSG00000236353      5089
## 19286            PBX2 ENSG00000232005      5089
## 19287            PBX2 ENSG00000224952      5089
## 19288            PBX2 ENSG00000206315      5089
## 19289            PBX2 ENSG00000237344      5089
## 19292           GPSM3 ENSG00000233490     63940
## 19293           GPSM3 ENSG00000237052     63940
## 19294           GPSM3 ENSG00000236697     63940
## 19295           GPSM3 ENSG00000234508     63940
## 19296           GPSM3 ENSG00000234243     63940
## 19297           GPSM3 ENSG00000206314     63940
## 19299          NOTCH4 ENSG00000238196      4855
## 19300          NOTCH4 ENSG00000232339      4855
## 19301          NOTCH4 ENSG00000223355      4855
## 19302          NOTCH4 ENSG00000235396      4855
## 19303          NOTCH4 ENSG00000234876      4855
## 19304          NOTCH4 ENSG00000206312      4855
## 19310           HCG23 ENSG00000235135    414764
## 19311           HCG23 ENSG00000230602    414764
## 19312           HCG23 ENSG00000228738    414764
## 19313           HCG23 ENSG00000229903    414764
## 19314           HCG23 ENSG00000224507    414764
## 19315           HCG23 ENSG00000226228    414764
## 19316           HCG23 ENSG00000225834    414764
## 19318           BTNL2 ENSG00000275798     56244
## 19319           BTNL2 ENSG00000226127     56244
## 19320           BTNL2 ENSG00000225845     56244
## 19321           BTNL2 ENSG00000229741     56244
## 19322           BTNL2 ENSG00000224242     56244
## 19323           BTNL2 ENSG00000225412     56244
## 19324           BTNL2 ENSG00000229597     56244
## 19325           BTNL2 ENSG00000224770     56244
## 19327         HLA-DRA ENSG00000277263      3122
## 19328         HLA-DRA ENSG00000234794      3122
## 19329         HLA-DRA ENSG00000226260      3122
## 19330         HLA-DRA ENSG00000230726      3122
## 19331         HLA-DRA ENSG00000228987      3122
## 19332         HLA-DRA ENSG00000227993      3122
## 19333         HLA-DRA ENSG00000206308      3122
## 19339        HLA-DRB1 ENSG00000229074      3123
## 19340        HLA-DRB1 ENSG00000228080      3123
## 19341        HLA-DRB1 ENSG00000236884      3123
## 19342        HLA-DRB1 ENSG00000206306      3123
## 19343        HLA-DRB1 ENSG00000206240      3123
## 19345        HLA-DQA1 ENSG00000225890      3117
## 19346        HLA-DQA1 ENSG00000233192      3117
## 19347        HLA-DQA1 ENSG00000236418      3117
## 19348        HLA-DQA1 ENSG00000231526      3117
## 19349        HLA-DQA1 ENSG00000206301      3117
## 19350        HLA-DQA1 ENSG00000257473      3117
## 19351        HLA-DQA1 ENSG00000223793      3117
## 19352        HLA-DQA1 ENSG00000231823      3117
## 19353        HLA-DQA1 ENSG00000232062      3117
## 19354        HLA-DQA1 ENSG00000228284      3117
## 19355        HLA-DQA1 ENSG00000225103      3117
## 19356        HLA-DQA1 ENSG00000206305      3117
## 19357        HLA-DQA1 ENSG00000237541      3117
## 19359        HLA-DQB1 ENSG00000206237      3119
## 19360        HLA-DQB1 ENSG00000231939      3119
## 19361        HLA-DQB1 ENSG00000231286      3119
## 19362        HLA-DQB1 ENSG00000225824      3119
## 19363        HLA-DQB1 ENSG00000233209      3119
## 19364        HLA-DQB1 ENSG00000206302      3119
## 19366    HLA-DQB1-AS1 ENSG00000238226 106480429
## 19367    HLA-DQB1-AS1 ENSG00000232351 106480429
## 19368    HLA-DQB1-AS1 ENSG00000231677 106480429
## 19369    HLA-DQB1-AS1 ENSG00000233744 106480429
## 19370    HLA-DQB1-AS1 ENSG00000230414 106480429
## 19371    HLA-DQB1-AS1 ENSG00000237455 106480429
## 19377        HLA-DQA2 ENSG00000233192      3118
## 19378        HLA-DQA2 ENSG00000231526      3118
## 19379        HLA-DQA2 ENSG00000206301      3118
## 19380        HLA-DQA2 ENSG00000257473      3118
## 19381        HLA-DQA2 ENSG00000223793      3118
## 19382        HLA-DQA2 ENSG00000231823      3118
## 19383        HLA-DQA2 ENSG00000225103      3118
## 19386        HLA-DQB2 ENSG00000230675      3120
## 19387        HLA-DQB2 ENSG00000226165      3120
## 19388        HLA-DQB2 ENSG00000229493      3120
## 19389        HLA-DQB2 ENSG00000228813      3120
## 19390        HLA-DQB2 ENSG00000228254      3120
## 19391        HLA-DQB2 ENSG00000224305      3120
## 19392        HLA-DQB2 ENSG00000196610      3120
## 19394         HLA-DOB ENSG00000243612      3112
## 19395         HLA-DOB ENSG00000241910      3112
## 19396         HLA-DOB ENSG00000243496      3112
## 19397         HLA-DOB ENSG00000239457      3112
## 19398         HLA-DOB ENSG00000241386      3112
## 19400            TAP2 ENSG00000225967      6891
## 19401            TAP2 ENSG00000206235      6891
## 19402            TAP2 ENSG00000232326      6891
## 19403            TAP2 ENSG00000223481      6891
## 19404            TAP2 ENSG00000228582      6891
## 19405            TAP2 ENSG00000206299      6891
## 19406            TAP2 ENSG00000237599      6891
## 19408           PSMB8 ENSG00000230669      5696
## 19409           PSMB8 ENSG00000231631      5696
## 19410           PSMB8 ENSG00000236443      5696
## 19411           PSMB8 ENSG00000206298      5696
## 19412           PSMB8 ENSG00000230034      5696
## 19413           PSMB8 ENSG00000226201      5696
## 19414           PSMB8 ENSG00000235715      5696
## 19417           PSMB9 ENSG00000239836      5698
## 19418           PSMB9 ENSG00000243958      5698
## 19419           PSMB9 ENSG00000242711      5698
## 19420           PSMB9 ENSG00000240508      5698
## 19421           PSMB9 ENSG00000243594      5698
## 19422           PSMB9 ENSG00000240118      5698
## 19423           PSMB9 ENSG00000243067      5698
## 19425            TAP1 ENSG00000227816      6890
## 19426            TAP1 ENSG00000232367      6890
## 19427            TAP1 ENSG00000226173      6890
## 19428            TAP1 ENSG00000224748      6890
## 19429            TAP1 ENSG00000230705      6890
## 19430            TAP1 ENSG00000224212      6890
## 19431            TAP1 ENSG00000206297      6890
## 19435         HLA-DMB ENSG00000242092      3109
## 19436         HLA-DMB ENSG00000242386      3109
## 19437         HLA-DMB ENSG00000234154      3109
## 19438         HLA-DMB ENSG00000241296      3109
## 19439         HLA-DMB ENSG00000226264      3109
## 19440         HLA-DMB ENSG00000239329      3109
## 19441         HLA-DMB ENSG00000241674      3109
## 19445         HLA-DMA ENSG00000242361      3108
## 19446         HLA-DMA ENSG00000239463      3108
## 19447         HLA-DMA ENSG00000241394      3108
## 19448         HLA-DMA ENSG00000243189      3108
## 19449         HLA-DMA ENSG00000243215      3108
## 19450         HLA-DMA ENSG00000242685      3108
## 19451         HLA-DMA ENSG00000243719      3108
## 19453            BRD2 ENSG00000234704      6046
## 19454            BRD2 ENSG00000235307      6046
## 19455            BRD2 ENSG00000230678      6046
## 19456            BRD2 ENSG00000236227      6046
## 19457            BRD2 ENSG00000234507      6046
## 19458            BRD2 ENSG00000215077      6046
## 19462         HLA-DOA ENSG00000232957      3111
## 19463         HLA-DOA ENSG00000235744      3111
## 19464         HLA-DOA ENSG00000231558      3111
## 19465         HLA-DOA ENSG00000206292      3111
## 19466         HLA-DOA ENSG00000232962      3111
## 19467         HLA-DOA ENSG00000230141      3111
## 19469        HLA-DPA1 ENSG00000228163      3113
## 19470        HLA-DPA1 ENSG00000235844      3113
## 19471        HLA-DPA1 ENSG00000229685      3113
## 19472        HLA-DPA1 ENSG00000206291      3113
## 19473        HLA-DPA1 ENSG00000236177      3113
## 19474        HLA-DPA1 ENSG00000168384      3113
## 19475        HLA-DPA1 ENSG00000224103      3113
## 19477        HLA-DPB1 ENSG00000236693      3115
## 19478        HLA-DPB1 ENSG00000230708      3115
## 19479        HLA-DPB1 ENSG00000229295      3115
## 19480        HLA-DPB1 ENSG00000226826      3115
## 19481        HLA-DPB1 ENSG00000215048      3115
## 19482        HLA-DPB1 ENSG00000230763      3115
## 19483        HLA-DPB1 ENSG00000237710      3115
## 19488        HLA-DPB2 ENSG00000226071      3116
## 19489        HLA-DPB2 ENSG00000223372      3116
## 19490        HLA-DPB2 ENSG00000233584      3116
## 19491        HLA-DPB2 ENSG00000225429      3116
## 19492        HLA-DPB2 ENSG00000168379      3116
## 19493        HLA-DPB2 ENSG00000234834      3116
## 19494        HLA-DPB2 ENSG00000225132      3116
## 19498         COL11A2 ENSG00000235708      1302
## 19499         COL11A2 ENSG00000232541      1302
## 19500         COL11A2 ENSG00000223699      1302
## 19501         COL11A2 ENSG00000206290      1302
## 19502         COL11A2 ENSG00000230930      1302
## 19503         COL11A2 ENSG00000227801      1302
## 19505            RXRB ENSG00000231321      6257
## 19506            RXRB ENSG00000235712      6257
## 19507            RXRB ENSG00000228333      6257
## 19508            RXRB ENSG00000227322      6257
## 19509            RXRB ENSG00000206289      6257
## 19512         SLC39A7 ENSG00000229802      7922
## 19513         SLC39A7 ENSG00000227402      7922
## 19514         SLC39A7 ENSG00000206288      7922
## 19515         SLC39A7 ENSG00000226614      7922
## 19516         SLC39A7 ENSG00000224399      7922
## 19518         HSD17B8 ENSG00000228357      7923
## 19519         HSD17B8 ENSG00000225312      7923
## 19520         HSD17B8 ENSG00000232357      7923
## 19521         HSD17B8 ENSG00000112474      7923
## 19522         HSD17B8 ENSG00000228712      7923
## 19525           RING1 ENSG00000228520      6015
## 19526           RING1 ENSG00000235107      6015
## 19527           RING1 ENSG00000226788      6015
## 19528           RING1 ENSG00000231115      6015
## 19529           RING1 ENSG00000206287      6015
## 19534           HCG25 ENSG00000231037    414765
## 19535           HCG25 ENSG00000231343    414765
## 19536           HCG25 ENSG00000238064    414765
## 19537           HCG25 ENSG00000224096    414765
## 19538           HCG25 ENSG00000231573    414765
## 19539           HCG25 ENSG00000233772    414765
## 19541           VPS52 ENSG00000224455      6293
## 19542           VPS52 ENSG00000223618      6293
## 19543           VPS52 ENSG00000236014      6293
## 19544           VPS52 ENSG00000228425      6293
## 19545           VPS52 ENSG00000225590      6293
## 19546           VPS52 ENSG00000206286      6293
## 19548           RPS18 ENSG00000227794      6222
## 19549           RPS18 ENSG00000223367      6222
## 19550           RPS18 ENSG00000226225      6222
## 19551           RPS18 ENSG00000096150      6222
## 19552           RPS18 ENSG00000235650      6222
## 19554         B3GALT4 ENSG00000235155      8705
## 19555         B3GALT4 ENSG00000206285      8705
## 19556         B3GALT4 ENSG00000236802      8705
## 19557         B3GALT4 ENSG00000226936      8705
## 19559           WDR46 ENSG00000226916      9277
## 19560           WDR46 ENSG00000236222      9277
## 19561           WDR46 ENSG00000204221      9277
## 19562           WDR46 ENSG00000206284      9277
## 19564           PFDN6 ENSG00000235692     10471
## 19565           PFDN6 ENSG00000237335     10471
## 19566           PFDN6 ENSG00000206283     10471
## 19567           PFDN6 ENSG00000224782     10471
## 19569            RGL2 ENSG00000237825      5863
## 19570            RGL2 ENSG00000228736      5863
## 19571            RGL2 ENSG00000206282      5863
## 19572            RGL2 ENSG00000224841      5863
## 19574           TAPBP ENSG00000206281      6892
## 19575           TAPBP ENSG00000236490      6892
## 19576           TAPBP ENSG00000112493      6892
## 19577           TAPBP ENSG00000206208      6892
## 19579          ZBTB22 ENSG00000206280      9278
## 19580          ZBTB22 ENSG00000229253      9278
## 19581          ZBTB22 ENSG00000237056      9278
## 19582          ZBTB22 ENSG00000227780      9278
## 19584            DAXX ENSG00000231617      1616
## 19585            DAXX ENSG00000229396      1616
## 19586            DAXX ENSG00000206206      1616
## 19587            DAXX ENSG00000227046      1616
## 19588            DAXX ENSG00000206279      1616
## 19593           KIFC1 ENSG00000233450      3833
## 19594           KIFC1 ENSG00000056678      3833
## 19595           KIFC1 ENSG00000204197      3833
## 19598            PHF1 ENSG00000225553      5252
## 19599            PHF1 ENSG00000239756      5252
## 19601            CUTA ENSG00000226492     51596
## 19603         SYNGAP1 ENSG00000227460      8831
## 19606           ZBTB9 ENSG00000236515    221504
## 19712         TMEM217 ENSG00000286105    221468
## 20008           RN7SK ENSG00000283293    125050
## 20117          PTP4A1 ENSG00000285976      7803
## 20315            IBTK ENSG00000283068     25998
## 20319            TPBG ENSG00000283085      7162
## 20429            MDN1 ENSG00000288121     23195
## 20434        CASP8AP2 ENSG00000288475      9994
## 20438           GJA10 ENSG00000288435     84694
## 20853           SOGA3 ENSG00000255330    387104
## 20861          THEMIS ENSG00000275122    387357
## 20863           PTPRK ENSG00000273993      5796
## 21153            TAB2 ENSG00000228408     23118
## 21178          RAET1E ENSG00000285991    135250
## 21180      RAET1E-AS1 ENSG00000268592 100652739
## 21477          ERMARD ENSG00000276187     55780
## 21480       LINC00242 ENSG00000280868    401288
## 21482       LINC00574 ENSG00000281305     80069
## 21491            DLL1 ENSG00000275555     28514
## 21493         FAM120B ENSG00000275333     84498
## 21498           PSMB1 ENSG00000281184      5689
## 21515          FAM20C ENSG00000281429     56975
## 21516          FAM20C ENSG00000282147     56975
## 21517          FAM20C ENSG00000288499     56975
## 21606            MMD2            <NA> 100505381
## 21982            CHN2 ENSG00000285162      1124
## 22711          TRIM74 ENSG00000174353    378108
## 22826            DTX2 ENSG00000282379    113878
## 22830           UPK3B ENSG00000276184 105375355
## 22836          POMZP3 ENSG00000276464     22932
## 23113          SMURF1 ENSG00000284126     57154
## 23115           KPNA7 ENSG00000284068    402569
## 23300          ARMC10 ENSG00000282813     83787
## 23303         NAPEPLD ENSG00000275723    222236
## 23307       DPY19L2P2 ENSG00000282026    349152
## 23359         PRKAR2B ENSG00000284096      5577
## 23362            HBP1 ENSG00000283847     26959
## 23365            COG5 ENSG00000284369     10466
## 23369           GPR22 ENSG00000283812      2845
## 23371           DUS4L ENSG00000284103     11062
## 23374          BCAP29 ENSG00000283852     55973
## 23865             AGK ENSG00000262327     55750
## 23870        WEE2-AS1 ENSG00000261994    285962
## 23872            WEE2 ENSG00000263042    494551
## 23875           SSBP1 ENSG00000262771      6742
## 23889            MGAM ENSG00000282607      8972
## 23897          PRSS58 ENSG00000276785    136541
## 23943        MTRNR2L6 ENSG00000270672 100463482
## 23953           PRSS1 ENSG00000274247      5644
## 23968           EPHB6 ENSG00000275482      2051
## 23970           TRPV6 ENSG00000276971     55503
## 23973           TRPV5 ENSG00000274348     56302
## 23976             KEL ENSG00000276615      3792
## 23978           OR9A2 ENSG00000273914    135924
## 23981           OR6V1 ENSG00000277378    346517
## 23999             ZYX ENSG00000285443      7791
## 24001           EPHA1 ENSG00000284816      2041
## 24003       EPHA1-AS1 ENSG00000285468    285965
## 24006         TAS2R60 ENSG00000285341    338398
## 24008         TAS2R41 ENSG00000284982    259287
## 24014         CTAGE15 ENSG00000285172    441294
## 24023          CTAGE6 ENSG00000285123    340307
## 24028           OR2F2 ENSG00000284965    135948
## 24031           OR2F1 ENSG00000284866     26211
## 24036           OR6B1 ENSG00000284939    135946
## 24038           OR2A5 ENSG00000284896    393046
## 24040          OR2A25 ENSG00000285496    392138
## 24043          OR2A12 ENSG00000284949    346525
## 24045           OR2A2 ENSG00000285071    442361
## 24048          OR2A14 ENSG00000284891    135941
## 24054          CTAGE4 ENSG00000288370 100128553
## 24056        ARHGEF35 ENSG00000288422    445328
## 24059          OR2A42 ENSG00000284836    402317
## 24063           OR2A7 ENSG00000284749    401427
## 24065          CTAGE8 ENSG00000288181 100142659
## 24069           OR2A1 ENSG00000285105    346528
## 24071         ARHGEF5 ENSG00000284933      7984
## 24073           NOBOX ENSG00000285328    135935
## 24087         CNTNAP2 ENSG00000278728     26047
## 24294          PTPRN2 ENSG00000282185      5799
## 24318         PPP2R3B ENSG00000273850     28227
## 24319         PPP2R3B ENSG00000276438     28227
## 24987         GAGE12I ENSG00000215269     26748
## 25479           TBX22 ENSG00000277800     50945
## 25740           RAB9B ENSG00000288597     51209
## 25746         TMSB15B ENSG00000269226    286527
## 25977           MCTS1 ENSG00000288295     28985
## 25979       C1GALT1C1 ENSG00000288368     29071
## 25983          CT47B1 ENSG00000288466    643311
## 25988         CT47A11 ENSG00000288273    255313
## 25989         CT47A11 ENSG00000226023    255313
## 26001          CT47A6 ENSG00000288273    728062
## 26005          CT47A4 ENSG00000288477    728075
## 26010          CT47A1 ENSG00000288363    728096
## 26016           GLUD2 ENSG00000288118      2747
## 26624        DDX11L16 ENSG00000233614    727856
## 26625        DDX11L16 ENSG00000248472    727856
## 26626        DDX11L16 ENSG00000223972    727856
## 26648          ERICH1 ENSG00000282665    157697
## 26656          DLGAP2 ENSG00000282103      9228
## 26657          DLGAP2 ENSG00000282152      9228
## 26658          DLGAP2 ENSG00000274161      9228
## 26659          DLGAP2 ENSG00000282318      9228
## 26663            CLN8 ENSG00000278220      2055
## 26667        ARHGEF10 ENSG00000274726      9639
## 26669     KBTBD11-OT1 ENSG00000282334 104266957
## 26670     KBTBD11-OT1 ENSG00000283239 104266957
## 26673         KBTBD11 ENSG00000273645      9920
## 26677           MYOM2 ENSG00000274137      9172
## 26700           MCPH1 ENSG00000285262     79648
## 26707          AGPAT5 ENSG00000284980     55326
## 26709        MIR4659B ENSG00000285083 100616372
## 26711            XKR5 ENSG00000285327    389610
## 26713      GS1-24F4.2 ENSG00000285156 100652791
## 26715           DEFB1 ENSG00000284881      1672
## 26718           DEFA6 ENSG00000285136      1671
## 26721           DEFA4 ENSG00000285318      1669
## 26723          DEFA8P ENSG00000284863    449491
## 26725          DEFA9P ENSG00000284789    449492
## 26727         DEFA10P ENSG00000233531    449493
## 26729           DEFA1 ENSG00000284983      1667
## 26732          DEFA1B ENSG00000285176    728358
## 26734         DEFT1P2 ENSG00000215378 100287083
## 26736           DEFA3 ENSG00000284835      1668
## 26740           DEFA5 ENSG00000285251      1670
## 26762         USP17L4 ENSG00000284781    645402
## 26765         ZNF705G ENSG00000274195 100131980
## 26766         ZNF705G ENSG00000285286 100131980
## 26769          DEFB4B ENSG00000275444 100289462
## 26770          DEFB4B ENSG00000285433 100289462
## 26771          DEFB4B ENSG00000285181 100289462
## 26772          DEFB4B ENSG00000171711 100289462
## 26775        DEFB103B ENSG00000273641     55894
## 26776        DEFB103B ENSG00000284978     55894
## 26777        DEFB103B ENSG00000176797     55894
## 26779         SPAG11B ENSG00000274405     10407
## 26780         SPAG11B ENSG00000288309     10407
## 26783        DEFB104B ENSG00000277006    503618
## 26784        DEFB104B ENSG00000285356    503618
## 26786        DEFB106B ENSG00000275794    503841
## 26787        DEFB106B ENSG00000284937    503841
## 26789        DEFB105B ENSG00000274729    504180
## 26790        DEFB105B ENSG00000285015    504180
## 26791        DEFB105B ENSG00000285411    504180
## 26793        DEFB107B ENSG00000277530    503614
## 26794        DEFB107B ENSG00000284979    503614
## 26795        DEFB107B ENSG00000285432    503614
## 26796        DEFB107B ENSG00000186572    503614
## 26818        DEFB107A ENSG00000277530    245910
## 26819        DEFB107A ENSG00000284979    245910
## 26820        DEFB107A ENSG00000285432    245910
## 26821        DEFB107A ENSG00000198129    245910
## 26823        DEFB105A ENSG00000274729    245908
## 26824        DEFB105A ENSG00000285015    245908
## 26825        DEFB105A ENSG00000186599    245908
## 26827        DEFB106A ENSG00000285617    245909
## 26829        DEFB104A ENSG00000285034    140596
## 26831         SPAG11A ENSG00000285507    653423
## 26834        DEFB103A ENSG00000285376    414325
## 26835        DEFB103A ENSG00000284978    414325
## 26838          DEFB4A ENSG00000275444      1673
## 26839          DEFB4A ENSG00000285433      1673
## 26840          DEFB4A ENSG00000285181      1673
## 26841          DEFB4A ENSG00000177257      1673
## 26843         ZNF705B ENSG00000285120 100132396
## 26848         USP17L8 ENSG00000284781    392188
## 26849         USP17L8 ENSG00000236125    392188
## 26851         USP17L3 ENSG00000284806    645836
## 26867        FAM86B3P ENSG00000285119    286042
## 26878          CLDN23 ENSG00000285098    137075
## 26882          MFHAS1 ENSG00000285022      9258
## 26888         MIR4660 ENSG00000285514 100616350
## 26891         PPP1R3B ENSG00000285343     79660
## 26906            TNKS ENSG00000285372      8658
## 26909          MIR597 ENSG00000285033    693182
## 26913            MSRA ENSG00000285250      4482
## 26923          PRSS55 ENSG00000285141    203074
## 26926         MIR4286 ENSG00000285364 100422982
## 26928         C8orf74 ENSG00000285147    203076
## 26931            SOX7 ENSG00000285438     83595
## 26934           PINX1 ENSG00000284764     54984
## 26935           PINX1 ENSG00000258724     54984
## 26939          MIR598 ENSG00000285056    693183
## 26952           MTMR9 ENSG00000285032     66036
## 26955         SLC35G5 ENSG00000285084     83650
## 26957             TDH ENSG00000284856    157739
## 26964             BLK ENSG00000285369       640
## 26971           GATA4 ENSG00000285109      2626
## 26976           FDFT1 ENSG00000284967      2222
## 26979            CTSB ENSG00000285132      1508
## 26985         DEFB136 ENSG00000285087    613210
## 26987         DEFB135 ENSG00000285365    613209
## 26989         DEFB134 ENSG00000284754    613211
## 27000         ZNF705D ENSG00000285124    728957
## 27004         USP17L7 ENSG00000285497    392197
## 27006         USP17L2 ENSG00000284990    377630
## 27027         FAM86B2 ENSG00000285397    653333
## 27042       MIR5692A2 ENSG00000284785 100847038
## 27044          LONRF1 ENSG00000285360     91694
## 27046       MIR3926-2 ENSG00000284855 100500838
## 27049       LINC00681 ENSG00000285297 101409254
## 27055            DLC1 ENSG00000288673     10395
## 27502           ADAM9 ENSG00000282230      8754
## 27504          ADAM32 ENSG00000275594    203102
## 27513          ADAM18 ENSG00000278548      8749
## 27515           ADAM2 ENSG00000276286      2515
## 27781       LINC00588 ENSG00000215117     26138
## 28771           GSDMC ENSG00000285114     56169
## 28871           GPR20 ENSG00000275181      2843
## 28874          PTP4A3 ENSG00000275575     11156
## 28876           MROH5 ENSG00000282181    389690
## 28913            LY6E ENSG00000278032      4061
## 28919            LY6H ENSG00000274488      4062
## 28935           ZC3H3 ENSG00000282684     23144
## 28938           GSDMD ENSG00000278718     79792
## 28940           MROH6 ENSG00000277781    642475
## 28945           EEF1D ENSG00000273594      1936
## 28947           TIGD5 ENSG00000278016     84948
## 28953          ZNF623 ENSG00000276340      9831
## 28956          ZNF707 ENSG00000274352    286075
## 28959         CCDC166 ENSG00000278749 100130274
## 28962          MAPK15 ENSG00000274205    225689
## 28965          FAM83H ENSG00000273889    286077
## 28971           SCRIB ENSG00000274287     23513
## 28974           PUF60 ENSG00000274081     22827
## 29003            BOP1 ENSG00000285301     23246
## 29006            HSF1 ENSG00000284774      3297
## 29009           DGAT1 ENSG00000285482      8694
## 29011           SCRT1 ENSG00000284923     83482
## 29013         TMEM249 ENSG00000285272    340393
## 29015         SLC52A2 ENSG00000285112     79581
## 29017           FBXL6 ENSG00000285442     26233
## 29019           ADCK5 ENSG00000285451    203054
## 29021           CPSF1 ENSG00000285049     29894
## 29023          MIR939 ENSG00000284918 100126351
## 29025         MIR1234 ENSG00000285207 100302196
## 29028         SLC39A4 ENSG00000285243     55630
## 29030           VPS28 ENSG00000285339     51160
## 29056          ZNF251 ENSG00000278062     90987
## 29074         DDX11L5 ENSG00000248472 100287596
## 29075         DDX11L5 ENSG00000223972 100287596
## 29218           PTPRD ENSG00000282932      5789
## 29664          FBXO10 ENSG00000256966     26267
## 30048           APBA1 ENSG00000276497       320
## 30057          MAMDC2 ENSG00000278608    256691
## 30261       SPATA31C1 ENSG00000177910    441452
## 30430         SLC35D2 ENSG00000285269     11046
## 30531            BAAT ENSG00000276559       570
## 30957      ST6GALNAC6 ENSG00000257524     30815
## 31129           OBP2B ENSG00000280584     29989
## 31135           SURF6 ENSG00000281309      6838
## 31137           MED22 ENSG00000281022      6837
## 31140           RPL7A ENSG00000280858      6130
## 31142         SNORD24 ENSG00000280889     26820
## 31145        SNORD36A ENSG00000281907     26815
## 31147        SNORD36C ENSG00000281541     26813
## 31149           SURF1 ENSG00000280627      6834
## 31151           SURF2 ENSG00000281024      6835
## 31153           SURF4 ENSG00000280951      6836
## 31156           REXO4 ENSG00000280706     57109
## 31158        ADAMTS13 ENSG00000281244     11093
## 31160          CACFD1 ENSG00000280479     11094
## 31162          SLC2A6 ENSG00000281165     11182
## 31756          PTCHD3 ENSG00000276595    374308
## 31939       HSD17B7P2 ENSG00000288374    158160
## 32044          OR13A1 ENSG00000277495     79290
## 32046           ALOX5 ENSG00000275565       240
## 32135          FAM25C ENSG00000288481    644054
## 32485      DNAJC9-AS1 ENSG00000236756    414245
## 32523           NDST2 ENSG00000272916      8509
## 32545           KAT6B ENSG00000281813     23522
## 32590            DLG5 ENSG00000274429      9231
## 32755           ATAD1 ENSG00000283024     84896
## 32757          CFL1P1 ENSG00000282866    142913
## 32760            KLLN ENSG00000283059 100144748
## 32762            PTEN ENSG00000284792      5728
## 33559          PTDSS2 ENSG00000282367     81490
## 33562            RNH1 ENSG00000276230      6050
## 33565            HRAS ENSG00000276536      3265
## 33567          LRRC56 ENSG00000273831    115399
## 33571          RASSF7 ENSG00000273859      8045
## 33573        MIR210HG ENSG00000282810 100506211
## 33576           PHRF1 ENSG00000274780     57661
## 33578            IRF7 ENSG00000276561      3665
## 33580           CDHR5 ENSG00000273572     53841
## 33582             SCT ENSG00000274473      6343
## 33584            DRD4 ENSG00000276825      1815
## 33586           DEAF1 ENSG00000282712     10522
## 33610           AP2A2 ENSG00000280759       161
## 33611           AP2A2 ENSG00000281385       161
## 33615            MUC6 ENSG00000277518      4588
## 33616            MUC6 ENSG00000277281      4588
## 33617            MUC6 ENSG00000283350      4588
## 33620            MUC2 ENSG00000278466      4583
## 33621            MUC2 ENSG00000284971      4583
## 33623          MUC5AC ENSG00000283158      4586
## 33632           DUSP8 ENSG00000278165      1850
## 33633           DUSP8 ENSG00000273793      1850
## 33635      KRTAP5-AS1 ENSG00000281176    338651
## 33636      KRTAP5-AS1 ENSG00000281801    338651
## 33638        KRTAP5-1 ENSG00000280585    387264
## 33639        KRTAP5-1 ENSG00000278210    387264
## 33641        KRTAP5-2 ENSG00000278489    440021
## 33642        KRTAP5-2 ENSG00000281533    440021
## 33644        KRTAP5-3 ENSG00000275920    387266
## 33645        KRTAP5-3 ENSG00000281191    387266
## 33647        KRTAP5-4 ENSG00000278620    387267
## 33648        KRTAP5-4 ENSG00000277068    387267
## 33650        KRTAP5-5 ENSG00000278302    439915
## 33651        KRTAP5-5 ENSG00000277291    439915
## 33654          FAM99A ENSG00000281261    387742
## 33655          FAM99A ENSG00000281733    387742
## 33658          FAM99B ENSG00000281783 100132464
## 33659          FAM99B ENSG00000281829 100132464
## 33662        KRTAP5-6 ENSG00000277389    440023
## 33664         IFITM10 ENSG00000281618    402778
## 33674            SYT8 ENSG00000288149     90019
## 33676           TNNI2 ENSG00000288219      7136
## 33678            LSP1 ENSG00000288199      4046
## 33680         MIR4298 ENSG00000288415 100423021
## 33685           TNNT3 ENSG00000288250      7140
## 33688          MRPL23 ENSG00000288141      6150
## 33690      MRPL23-AS1 ENSG00000288320 100133545
## 33693             H19 ENSG00000288237    283120
## 33697        INS-IGF2 ENSG00000284779    723961
## 33714           KCNQ1 ENSG00000282076      3784
## 33718       KCNQ1-AS1 ENSG00000282343    338653
## 33720         KCNQ1DN ENSG00000278855     55539
## 33722          CDKN1C ENSG00000273707      1028
## 33725        SLC22A18 ENSG00000276130      5002
## 33727          PHLDA2 ENSG00000274538      7262
## 33729          NAP1L4 ENSG00000273562      4676
## 33731         SNORA54 ENSG00000273525    677833
## 33853             HBD            <NA> 100187828
## 33983           OR5P2 ENSG00000276025    120065
## 33984           OR5P2 ENSG00000280931    120065
## 33986           OR5P3 ENSG00000278253    120066
## 33987           OR5P3 ENSG00000280808    120066
## 33991          OR10A6 ENSG00000276451    390093
## 33992          OR10A6 ENSG00000280899    390093
## 33994          OR10A3 ENSG00000273953     26496
## 33995          OR10A3 ENSG00000281680     26496
## 33997          NLRP10 ENSG00000276780    338322
## 33998          NLRP10 ENSG00000281166    338322
## 34197            SAA1 ENSG00000288411      6288
## 34200            HPS5 ENSG00000288445     11234
## 34202          GTF2H1 ENSG00000288114      2965
## 34204         MIR3159 ENSG00000288358 100423016
## 34206            LDHA ENSG00000288299      3939
## 34608          NDUFS3 ENSG00000285387      4722
## 34610          PTPMT1 ENSG00000285206    114971
## 34612          KBTBD4 ENSG00000284900     55709
## 34615         FAM180B ENSG00000284938    399888
## 34617         C1QTNF4 ENSG00000284838    114900
## 34619           MTCH2 ENSG00000285121     23788
## 34621           AGBL2 ENSG00000285501     79841
## 34623           FNBP4 ENSG00000285182     23360
## 34693          OR4C12 ENSG00000284255    283093
## 34789           OR5T2 ENSG00000262851    219464
## 34791           OR5T3 ENSG00000261897    390154
## 34793           OR5T1 ENSG00000262784    390155
## 34795           OR8H1 ENSG00000262611    219469
## 34798           OR8K3 ENSG00000262755    219473
## 34802           OR8K1 ENSG00000263328    390157
## 34805           OR8J1 ENSG00000262796    219477
## 34834           OR9G1 ENSG00000261958    390174
## 34838           OR9G4 ENSG00000262647    283189
## 34991           MS4A3 ENSG00000284903       932
## 35092            TUT1 ENSG00000255508     64852
## 35252           POLA2 ENSG00000285816     23649
## 35332           NPAS4 ENSG00000254510    266743
## 35484          PPFIA1 ENSG00000288198      8500
## 35488         MIR548K ENSG00000288233 100313770
## 35494            CTTN ENSG00000288401      2017
## 35546          LRTOMT ENSG00000284922    220074
## 35925         NAALAD2 ENSG00000285516     10003
## 35927         CHORDC1 ENSG00000285023     26973
## 36390           FOXR1 ENSG00000281277    283150
## 36398           RPS25 ENSG00000280831      6230
## 36400         TRAPPC4 ENSG00000280495     51399
## 36403         SLC37A4 ENSG00000281500      2542
## 36406           HYOU1 ENSG00000280682     10525
## 36410           VPS11 ENSG00000280616     55823
## 36750         FAM138D ENSG00000262927    677784
## 36752          IQSEC3 ENSG00000262607    440073
## 36784         MIR3649 ENSG00000284767 100500816
## 36786         ADIPOR2 ENSG00000285070     79602
## 36790        CACNA2D4 ENSG00000284953     93589
## 36792           LRTM2 ENSG00000285383    654429
## 36795       LINC00940 ENSG00000285233 100271702
## 36797           DCP1B ENSG00000284850    196513
## 36799         CACNA1C ENSG00000285479       775
## 36803     CACNA1C-IT2 ENSG00000285479 100874369
## 36804     CACNA1C-IT2 ENSG00000285266 100874369
## 36806     CACNA1C-AS4 ENSG00000285107 100874234
## 36811     CACNA1C-AS2 ENSG00000285101 100874235
## 36813     CACNA1C-AS1 ENSG00000285335 100652846
## 36959             C1R ENSG00000288512       715
## 36961            C1RL ENSG00000288124     51279
## 36963        C1RL-AS1 ENSG00000288352    283314
## 36966            RBP5 ENSG00000288369     83758
## 36969          CLSTN3 ENSG00000288427      9746
## 36972            PEX5 ENSG00000288217      5830
## 37000          CLEC4A ENSG00000284697     50856
## 37123          TAS2R7 ENSG00000273326     50837
## 37124          TAS2R7 ENSG00000274327     50837
## 37126          TAS2R8 ENSG00000272712     50836
## 37127          TAS2R8 ENSG00000277316     50836
## 37129          TAS2R9 ENSG00000273086     50835
## 37130          TAS2R9 ENSG00000273713     50835
## 37132            PRR4 ENSG00000263247     11272
## 37133            PRR4 ENSG00000282269     11272
## 37135         TAS2R10 ENSG00000272805     50839
## 37136         TAS2R10 ENSG00000277238     50839
## 37139            PRH1 ENSG00000263247      5554
## 37140            PRH1 ENSG00000282269      5554
## 37141            PRH1 ENSG00000277823      5554
## 37142            PRH1 ENSG00000111215      5554
## 37145         TAS2R13 ENSG00000273457     50838
## 37146         TAS2R13 ENSG00000277254     50838
## 37148            PRH2 ENSG00000272803      5555
## 37149            PRH2 ENSG00000275679      5555
## 37151         TAS2R14 ENSG00000261984     50840
## 37152         TAS2R14 ENSG00000276541     50840
## 37155         TAS2R50 ENSG00000273431    259296
## 37156         TAS2R50 ENSG00000276167    259296
## 37158         TAS2R20 ENSG00000273092    259295
## 37159         TAS2R20 ENSG00000282612    259295
## 37161         TAS2R19 ENSG00000263028    259294
## 37162         TAS2R19 ENSG00000278307    259294
## 37164         TAS2R31 ENSG00000263097    259290
## 37165         TAS2R31 ENSG00000282256    259290
## 37169         TAS2R46 ENSG00000262525    259292
## 37170         TAS2R46 ENSG00000278111    259292
## 37173         TAS2R43 ENSG00000262612    259289
## 37174         TAS2R43 ENSG00000282537    259289
## 37177         TAS2R30 ENSG00000262111    259293
## 37178         TAS2R30 ENSG00000274699    259293
## 37185         TAS2R42 ENSG00000273505    353164
## 37189            PRB3 ENSG00000275624      5544
## 37191            PRB4 ENSG00000274839      5545
## 37193            PRB1 ENSG00000275517      5542
## 37194            PRB1 ENSG00000282673      5542
## 37196            PRB2 ENSG00000275517    653247
## 37197            PRB2 ENSG00000282673    653247
## 37198            PRB2 ENSG00000251655    653247
## 37208         BCL2L14 ENSG00000281449     79370
## 37211            LRP6 ENSG00000281324      4040
## 37217          MANSC1 ENSG00000281818     54682
## 37220        LOH12CR2 ENSG00000281234    503693
## 37224          DUSP16 ENSG00000280962     80824
## 38017           HOXC5 ENSG00000273046      3222
## 38626          MGAT4C ENSG00000283530     25834
## 38627          MGAT4C ENSG00000285137     25834
## 38836            ANO4 ENSG00000262139    121601
## 38841          SLC5A8 ENSG00000262217    160728
## 39280           BCL7A ENSG00000282873       605
## 39283           MLXIP ENSG00000281178     22877
## 39342          DNAH10 ENSG00000281935    196385
## 39344          CCDC92 ENSG00000275035     80212
## 39443          PIWIL1 ENSG00000275051      9271
## 39488           DDX51 ENSG00000288503    317781
## 39490           NOC4L ENSG00000288146     79050
## 39494          GALNT9 ENSG00000288490     50614
## 39684         SPATA13 ENSG00000228741    221178
## 39685         SPATA13 ENSG00000273167    221178
## 40164       HNRNPA1L2 ENSG00000273784    144983
## 40567       NALCN-AS1 ENSG00000283035 100885778
## 40674       LINC01043 ENSG00000282706 101928752
## 40676       LINC01044 ENSG00000282737 104266956
## 40678          SPACA7 ENSG00000275865    122258
## 40680         TUBGCP3 ENSG00000282003     10426
## 40711           ATP4B ENSG00000288359       496
## 40713            GRK1 ENSG00000281988      6011
## 40714            GRK1 ENSG00000288263      6011
## 40716       LINC00552 ENSG00000282664 100130386
## 40717       LINC00552 ENSG00000288305 100130386
## 40719        TMEM255B ENSG00000282107    348013
## 40728           RASA3 ENSG00000280477     22821
## 41139       DHRS4-AS1 ENSG00000285282     55449
## 41141           DHRS4 ENSG00000284807     10901
## 41146           CPNE6 ENSG00000285221      9362
## 41148             NRL ENSG00000285493      4901
## 41150            PCK2 ENSG00000285241      5106
## 41152          DCAF11 ENSG00000284796     80344
## 41155           FITM1 ENSG00000285321    161247
## 41157           PSME1 ENSG00000284916      5720
## 41159            EMC9 ENSG00000285377     51016
## 41162           PSME2 ENSG00000284889      5721
## 41164           RNF31 ENSG00000285152     55072
## 41168            IRF9 ENSG00000285048     10379
## 41170            REC8 ENSG00000285007      9985
## 41172            IPO4 ENSG00000285248     79711
## 41175          TM9SF1 ENSG00000285465     10548
## 41177           TSSK4 ENSG00000285140    283629
## 41179          CHMP4A ENSG00000285302     29082
## 41182            MDP1 ENSG00000285200    145553
## 41184      NEDD8-MDP1 ENSG00000285425 100528064
## 41186           NEDD8 ENSG00000285246      4738
## 41188           GMPR2 ENSG00000284752     51292
## 41190           TINF2 ENSG00000284915     26277
## 41192            TGM1 ENSG00000285348      7051
## 41194         RABGGTA ENSG00000285193      5875
## 41196           DHRS1 ENSG00000284868    115817
## 41198            NOP9 ENSG00000285326    161424
## 41200           CIDEB ENSG00000285199     27141
## 41202          LTB4R2 ENSG00000285203     56413
## 41204           LTB4R ENSG00000285456      1241
## 41206           ADCY4 ENSG00000284814    196883
## 41209           RIPK3 ENSG00000285379     11035
## 41212          NFATC4 ENSG00000285485      4776
## 41381           SFTA3 ENSG00000257520    253970
## 41493       LINC00871 ENSG00000288232 100506412
## 41811           SGPP1 ENSG00000285281     81537
## 41842     CHURC1-FNTB ENSG00000257365 100529261
## 42016           PTGR2 ENSG00000258653    145482
## 42291        CATSPERB ENSG00000274338     79820
## 42297            TC2N ENSG00000276776    123036
## 42315            CHGA ENSG00000276781      1113
## 42317           ITPK1 ENSG00000274958      3705
## 42319       ITPK1-AS1 ENSG00000280802    319085
## 42322           MOAP1 ENSG00000278268     64112
## 42324         TMEM251 ENSG00000275947     26175
## 42328            UBR7 ENSG00000278787     55148
## 42331           BTBD7 ENSG00000277222     55727
## 42334           UNC79 ENSG00000276416     57578
## 42336           COX8C ENSG00000277018    341947
## 42339          PRIMA1 ENSG00000274089    145270
## 42341     FAM181A-AS1 ENSG00000281032    283592
## 42343         FAM181A ENSG00000273533     90050
## 42345            ASB2 ENSG00000278693     51676
## 42350           OTUB2 ENSG00000277276     78990
## 42352           DDX24 ENSG00000273761     57062
## 42354         IFI27L1 ENSG00000276880    122509
## 42356           IFI27 ENSG00000275214      3429
## 42358         IFI27L2 ENSG00000276879     83982
## 42360          PPP4R4 ENSG00000278326     57718
## 42362       SERPINA10 ENSG00000278767     51156
## 42364        SERPINA6 ENSG00000277405       866
## 42367        SERPINA1 ENSG00000277377      5265
## 42711         TMEM179 ENSG00000276342    388021
## 42713       C14orf180 ENSG00000274126    400258
## 42827           ADAM6 ENSG00000282626      8755
## 43003          POTEB2 ENSG00000288113 100287399
## 43035           POTEB ENSG00000288347 100996331
## 43039           NF1P2 ENSG00000281347    440225
## 43050           OR4M2 ENSG00000288194    390538
## 43052           OR4N4 ENSG00000288501    283694
## 43069        GOLGA8DP ENSG00000278508 100132979
## 43070        GOLGA8DP ENSG00000278070 100132979
## 43071        GOLGA8DP ENSG00000288344 100132979
## 43075        GOLGA6L1 ENSG00000278247    283767
## 43076        GOLGA6L1 ENSG00000275009    283767
## 43077        GOLGA6L1 ENSG00000288214    283767
## 43082         TUBGCP5 ENSG00000280807    114791
## 43083         TUBGCP5 ENSG00000276856    114791
## 43085          CYFIP1 ENSG00000280618     23191
## 43086          CYFIP1 ENSG00000288461     23191
## 43089           NIPA1 ENSG00000288478    123606
## 43105        GOLGA8EP ENSG00000185182    390535
## 43117        GOLGA6L2 ENSG00000288517    283685
## 43122          MAGEL2 ENSG00000288188     54551
## 43125             NDN ENSG00000288364      4692
## 43251            OCA2 ENSG00000277361      4948
## 43255           HERC2 ENSG00000277278      8924
## 43256           HERC2 ENSG00000276802      8924
## 43263         GOLGA8F ENSG00000276896 100132565
## 43264         GOLGA8F ENSG00000278310 100132565
## 43274         GOLGA8G ENSG00000273651    283768
## 43275         GOLGA8G ENSG00000277090    283768
## 43283         HERC2P9 ENSG00000282417    440248
## 43286         GOLGA8M ENSG00000278186    653720
## 43287         GOLGA8M ENSG00000261480    653720
## 43300           APBA2 ENSG00000276495       321
## 43303        FAM189A1 ENSG00000273564     23359
## 43312            TJP1 ENSG00000277401      7082
## 43321         GOLGA8J ENSG00000278119    653073
## 43326          ULK4P3 ENSG00000282509     89837
## 43328         GOLGA8T ENSG00000284076    653075
## 43340        CHRFAM7A ENSG00000275917     89832
## 43351         GOLGA8Q ENSG00000282773    727909
## 43356          ULK4P2 ENSG00000282689 100288380
## 43364       ARHGAP11B ENSG00000274734     89839
## 43365       ARHGAP11B ENSG00000286139     89839
## 43366       ARHGAP11B ENSG00000285077     89839
## 43375            FAN1 ENSG00000276787     22909
## 43378          MTMR10 ENSG00000277086     54893
## 43381           TRPM1 ENSG00000274965      4308
## 43387           KLF13 ENSG00000275746     51621
## 43393          CHRNA7 ENSG00000274542      1139
## 43394          CHRNA7 ENSG00000282088      1139
## 43401         GOLGA8K ENSG00000284076    653125
## 43402         GOLGA8K ENSG00000261247    653125
## 43408          ULK4P1 ENSG00000282689     89838
## 43409          ULK4P1 ENSG00000260128     89838
## 43412         GOLGA8O ENSG00000282773    728047
## 43413         GOLGA8O ENSG00000178115    728047
## 43423         GOLGA8N ENSG00000283589    643699
## 43431       ARHGAP11A ENSG00000275568      9824
## 43433            SCG5 ENSG00000277614      6447
## 43434            SCG5 ENSG00000281931      6447
## 43438           GREM1 ENSG00000276886     26585
## 43439           GREM1 ENSG00000282046     26585
## 43659          LRRC57 ENSG00000285942    255252
## 43736           PATL2 ENSG00000282077    197135
## 43738             B2M ENSG00000273686       567
## 43740          TRIM69 ENSG00000278211    140691
## 43955         ZNF280D ENSG00000285253     54816
## 44154          MEGF11 ENSG00000277848     84465
## 44337            ISLR ENSG00000288508      3671
## 44339           STRA6 ENSG00000288257     64220
## 44342          CCDC33 ENSG00000288407     80125
## 44345         CYP11A1 ENSG00000288362      1583
## 44349          SEMA7A ENSG00000288455      8482
## 44351            UBL7 ENSG00000288408     84993
## 44569       GOLGA6L10 ENSG00000274166    647042
## 44570       GOLGA6L10 ENSG00000274042    647042
## 44572        UBE2Q2P2 ENSG00000259429 100134869
## 44576        GOLGA6L9 ENSG00000274320    440295
## 44584           RPS17 ENSG00000278229      6218
## 44606           CPEB1 ENSG00000277445     64506
## 44649        GOLGA6L4 ENSG00000274166    643707
## 44650        GOLGA6L4 ENSG00000278662    643707
## 44732            DET1 ENSG00000173867     55070
## 45030           OR4F4 ENSG00000288513     26682
## 45033         FAM138E ENSG00000288464 100124412
## 45035      MIR1302-10 ENSG00000288468 100422834
## 45038         DDX11L9 ENSG00000288170 100288486
## 45071           DECR2 ENSG00000274296     26063
## 45073       RAB11FIP3 ENSG00000275338      9727
## 45077          CAPN15 ENSG00000282214      6650
## 45184           MEIOB ENSG00000282650    254528
## 45190          HS3ST6 ENSG00000276333     64711
## 45278          PRSS21 ENSG00000282838     10942
## 45281           ZG16B ENSG00000283056    124220
## 45283         PRSS30P ENSG00000283070    124221
## 45285          PRSS22 ENSG00000282937     64063
## 45324           OR1F1 ENSG00000262668      4992
## 45366           GLIS2 ENSG00000274636     84662
## 45369           PAM16 ENSG00000282228     51025
## 45372     CORO7-PAM16 ENSG00000278760 100529144
## 45374           CORO7 ENSG00000282725     79585
## 45376            VASN ENSG00000274334    114990
## 45378          DNAJA3 ENSG00000276726      9093
## 45380          NMRAL1 ENSG00000274684     57407
## 45382           HMOX2 ENSG00000277424      3163
## 45384           CDIP1 ENSG00000274336     29965
## 45576            PARN ENSG00000274829      5073
## 45581            BFAR ENSG00000275618     51283
## 45584         PLA2G10 ENSG00000276870      8399
## 45587          NPIPA3 ENSG00000278308    642778
## 45591          NPIPA2 ENSG00000281994    642799
## 45592          NPIPA2 ENSG00000183426    642799
## 45595         ABCC6P2 ENSG00000273808    730013
## 45597           NOMO1 ENSG00000274779     23420
## 45605          NPIPA1 ENSG00000281994      9284
## 45607          PDXDC1 ENSG00000275498     23042
## 45612           NTAN1 ENSG00000275779    123803
## 45614            RRN3 ENSG00000278494     54700
## 45623          NPIPA5 ENSG00000282705 100288332
## 45626          MPV17L ENSG00000275543    255027
## 45627          MPV17L ENSG00000282074    255027
## 45628          MPV17L ENSG00000261130    255027
## 45633            NDE1 ENSG00000275911     54820
## 45637           MYH11 ENSG00000276480      4629
## 45645           ABCC1 ENSG00000278183      4363
## 45648           ABCC6 ENSG00000275331       368
## 45651           NOMO3 ENSG00000278087    408050
## 45662          NPIPA7 ENSG00000277983 101059938
## 45671           XYLT1 ENSG00000285395     64131
## 45754             ZP2 ENSG00000284588      7783
## 45756          ANKS4B ENSG00000284290    257629
## 45762          NPIPB3 ENSG00000169246     23117
## 45769          METTL9 ENSG00000284548     51108
## 45772           IGSF6 ENSG00000283934     10261
## 45783           PDZD9 ENSG00000284316    255762
## 45790           EEF2K ENSG00000284161     29904
## 45793          POLR3E ENSG00000284282     55718
## 45801          NPIPB5 ENSG00000284218 100132247
## 45844          TNRC6A ENSG00000288130     27327
## 45847         SLC5A11 ENSG00000288216    115584
## 45849        ARHGAP17 ENSG00000288353     55114
## 45908            CLN3 ENSG00000261832      1201
## 45957           BOLA2 ENSG00000169627    552900
## 46515          CES1P1 ENSG00000281948     51716
## 46517            CES1 ENSG00000262243      1066
## 46519           CES5A ENSG00000261972    221223
## 46831           SNTB2 ENSG00000260873      6645
## 46894           HYDIN ENSG00000283022     54768
## 46903           CALB2 ENSG00000282830       794
## 47003            ZFP1 ENSG00000285178    162239
## 47006           CTRB2 ENSG00000284810    440387
## 47008           CTRB1 ENSG00000285346      1504
## 47011           BCAR1 ENSG00000285460      9564
## 47356           DOC2B ENSG00000272670      8447
## 47359          RPH3AL ENSG00000262334      9501
## 47360          RPH3AL ENSG00000282013      9501
## 47367        C17orf97 ENSG00000283985    400566
## 47371           VPS53 ENSG00000283883     55275
## 47385             NXN ENSG00000281300     64359
## 47386             NXN ENSG00000280563     64359
## 47392          TIMM22 ENSG00000278501     29928
## 47393          TIMM22 ENSG00000277649     29928
## 47395             ABR ENSG00000276016        29
## 47396             ABR ENSG00000278741        29
## 47403           YWHAE ENSG00000274474      7531
## 47411         SLC43A2 ENSG00000278550    124935
## 47414          SCARF1 ENSG00000276336      8578
## 47416            RILP ENSG00000274145     83547
## 47418           PRPF8 ENSG00000274442     10594
## 47420           TLCD2 ENSG00000275246    727910
## 47422         MIR22HG ENSG00000282800     84981
## 47424           WDR81 ENSG00000276021    124997
## 47427        SERPINF2 ENSG00000276838      5345
## 47429        SERPINF1 ENSG00000282307      5176
## 47487           OR1D4 ENSG00000262628    653166
## 47657         CTDNEP1 ENSG00000288307     23399
## 47660            ELP5 ENSG00000288485     23587
## 47662           CLDN7 ENSG00000288292      1366
## 47664          SLC2A4 ENSG00000288174      6517
## 47667            YBX2 ENSG00000288504     51087
## 47669           EIF5A ENSG00000288145      1984
## 47671            GPS2 ENSG00000288325      2874
## 47674          NEURL4 ENSG00000288301     84461
## 47677           ACAP1 ENSG00000288169      9744
## 47679          KCTD11 ENSG00000288399    147040
## 47682          TMEM95 ENSG00000288511    339168
## 47684            TNK1 ENSG00000283781      8711
## 47688         TMEM256 ENSG00000283771    254863
## 47690           NLGN2 ENSG00000283859     57555
## 47693           SPEM1 ENSG00000284598    374768
## 47696         TMEM102 ENSG00000284228    284114
## 47699           FGF11 ENSG00000283903      2256
## 47703          CHRNB1 ENSG00000283946      1140
## 47705           ZBTB4 ENSG00000283868     57659
## 47707         SLC35G6 ENSG00000284515    643664
## 47709          POLR2A ENSG00000284832      5430
## 48022           LLGL1 ENSG00000284137      3996
## 48024            FLII ENSG00000284571      2314
## 48026           MIEF2 ENSG00000284495    125170
## 48029           TOP3A ENSG00000284238      7156
## 48033           SMCR8 ENSG00000283741    140775
## 48036           SHMT1 ENSG00000284320      6470
## 48038           EVPLL ENSG00000284166    645027
## 48053         LGALS9C ENSG00000284021    654346
## 48398          MYO18A ENSG00000221995    399687
## 48642           MMP28 ENSG00000278843     79148
## 48647           TAF15 ENSG00000276833      8148
## 48654            CCL5 ENSG00000274233      6352
## 48659            RDM1 ENSG00000276432    201299
## 48661           LYZL6 ENSG00000277042     57151
## 48665           CCL16 ENSG00000275095      6360
## 48667           CCL14 ENSG00000277236      6358
## 48671           CCL15 ENSG00000275528      6359
## 48675           CCL23 ENSG00000276114      6368
## 48677           CCL18 ENSG00000278006      6362
## 48678           CCL18 ENSG00000278167      6362
## 48681            CCL3 ENSG00000278567      6348
## 48682            CCL3 ENSG00000274221      6348
## 48684            CCL4 ENSG00000277943      6351
## 48685            CCL4 ENSG00000275824      6351
## 48690         TBC1D3B ENSG00000282750    414059
## 48691         TBC1D3B ENSG00000278632    414059
## 48692         TBC1D3B ENSG00000274939    414059
## 48695          CCL3L3 ENSG00000277796    414062
## 48696          CCL3L3 ENSG00000277768    414062
## 48697          CCL3L3 ENSG00000277336    414062
## 48699          CCL4L1 ENSG00000276070    388372
## 48704         TBC1D3H ENSG00000277974    729877
## 48706          CCL3L1 ENSG00000277768      6349
## 48707          CCL3L1 ENSG00000277336      6349
## 48708          CCL3L1 ENSG00000276085      6349
## 48710          CCL4L2 ENSG00000282604      9560
## 48711          CCL4L2 ENSG00000275313      9560
## 48712          CCL4L2 ENSG00000276125      9560
## 48714         TBC1D3G ENSG00000278632 101060321
## 48715         TBC1D3G ENSG00000275760 101060321
## 48716         TBC1D3G ENSG00000274939 101060321
## 48717         TBC1D3G ENSG00000274808 101060321
## 48721          ZNHIT3 ENSG00000278574      9326
## 48724           MYO19 ENSG00000278372     80179
## 48726            PIGW ENSG00000275600    284098
## 48728          GGNBP2 ENSG00000275099     79893
## 48731          DHRS11 ENSG00000275397     79154
## 48733            MRM1 ENSG00000274853     79922
## 48739            LHX1 ENSG00000274577      3975
## 48742            AATF ENSG00000276072     26574
## 48749           ACACA ENSG00000275176        31
## 48754        C17orf78 ENSG00000278145    284099
## 48757          TADA2A ENSG00000277104      6871
## 48761          DUSP14 ENSG00000275932     11072
## 48763           SYNRG ENSG00000274047     11276
## 48765           DDX52 ENSG00000277594     11056
## 48770           HNF1B ENSG00000276194      6928
## 48776         TBC1D3F ENSG00000282087     84218
## 48779          TBC1D3 ENSG00000276349    729873
## 48780          TBC1D3 ENSG00000274512    729873
## 48783          MRPL45 ENSG00000277936     84311
## 48785          GPR179 ENSG00000276469    440435
## 48787           SOCS7 ENSG00000274229     30837
## 48790        ARHGAP23 ENSG00000273780     57636
## 48793          SRCIN1 ENSG00000273608     80725
## 48801           MLLT6 ENSG00000275851      4302
## 48806           CISD3 ENSG00000274768    284106
## 48809           PCGF2 ENSG00000278644      7703
## 48812           PSMB3 ENSG00000275903      5691
## 48815         PIP4K2B ENSG00000277292      8396
## 48817           CWC25 ENSG00000276761     54883
## 48820        C17orf98 ENSG00000276913    388381
## 48914           KRT12 ENSG00000263243      3859
## 48916           KRT20 ENSG00000263057     54474
## 48919           KRT23 ENSG00000263309     25984
## 48921           KRT39 ENSG00000262164    390792
## 48923           KRT40 ENSG00000262845    125115
## 48925        KRTAP3-3 ENSG00000263101     85293
## 48927        KRTAP3-2 ENSG00000263296     83897
## 48930        KRTAP3-1 ENSG00000262068     83896
## 48932        KRTAP1-5 ENSG00000261862     83895
## 48934        KRTAP1-4 ENSG00000263242    728255
## 48936        KRTAP1-3 ENSG00000262347     81850
## 48938        KRTAP1-1 ENSG00000262808     81851
## 48940        KRTAP2-1 ENSG00000261852     81872
## 48942        KRTAP2-2 ENSG00000262731    728279
## 48944        KRTAP2-3 ENSG00000262862    730755
## 48946        KRTAP2-4 ENSG00000263091     85294
## 48950        KRTAP4-8 ENSG00000261968    728224
## 48953        KRTAP4-9 ENSG00000262121 100132386
## 48955       KRTAP4-11 ENSG00000263229    653240
## 48957       KRTAP4-12 ENSG00000263236     83755
## 48968        KRTAP9-2 ENSG00000263090     83899
## 48969        KRTAP9-2 ENSG00000262573     83899
## 48971        KRTAP9-3 ENSG00000262749     83900
## 48974        KRTAP9-4 ENSG00000262512     85280
## 48975        KRTAP9-4 ENSG00000262896     85280
## 48977        KRTAP9-9 ENSG00000267728     81870
## 48978        KRTAP9-9 ENSG00000262594     81870
## 48980        KRTAP9-6 ENSG00000267635 100507608
## 48981        KRTAP9-6 ENSG00000263263 100507608
## 48984        KRTAP9-7 ENSG00000262221 100505724
## 48987       KRTAP29-1 ENSG00000262218 100533177
## 48988       KRTAP29-1 ENSG00000262542 100533177
## 48990       KRTAP16-1 ENSG00000263186 100505753
## 48992       KRTAP17-1 ENSG00000263341     83902
## 48996          KRT33A ENSG00000261986      3883
## 48998          KRT33B ENSG00000263012      3884
## 49000           KRT34 ENSG00000262045      3885
## 49002           KRT31 ENSG00000262993      3881
## 49006           KRT37 ENSG00000263022      8688
## 49223         MAP3K14 ENSG00000282637      9020
## 49227        ARHGAP27 ENSG00000276836    201176
## 49228        ARHGAP27 ENSG00000276907    201176
## 49232         PLEKHM1 ENSG00000277111      9842
## 49233         PLEKHM1 ENSG00000276358      9842
## 49248           CRHR1 ENSG00000278232      1394
## 49249           CRHR1 ENSG00000282456      1394
## 49250           CRHR1 ENSG00000276191      1394
## 49251           CRHR1 ENSG00000263715      1394
## 49257          SPPL2C ENSG00000277106    162540
## 49258          SPPL2C ENSG00000278194    162540
## 49260            MAPT ENSG00000276155      4137
## 49261            MAPT ENSG00000277956      4137
## 49264             STH ENSG00000281139    246744
## 49266          KANSL1 ENSG00000275867    284058
## 49267          KANSL1 ENSG00000278458    284058
## 49271      KANSL1-AS1 ENSG00000281569    644246
## 49272      KANSL1-AS1 ENSG00000282799    644246
## 49277          ARL17B ENSG00000275748 100506084
## 49278          ARL17B ENSG00000276276 100506084
## 49280         LRRC37A ENSG00000278742      9884
## 49285        LRRC37A2 ENSG00000274332    474170
## 49286        LRRC37A2 ENSG00000277221    474170
## 49288          ARL17A ENSG00000275748     51326
## 49289          ARL17A ENSG00000276276     51326
## 49290          ARL17A ENSG00000228696     51326
## 49294             NSF ENSG00000278174      4905
## 49295             NSF ENSG00000276262      4905
## 49298            WNT3 ENSG00000277641      7473
## 49299            WNT3 ENSG00000277626      7473
## 49301           WNT9B ENSG00000276799      7484
## 49598           RNF43 ENSG00000285897     54894
## 49805        LRRC37A3 ENSG00000275621    374819
## 49937        SLC39A11 ENSG00000282291    201266
## 50265            GCGR ENSG00000288269      2642
## 50269         PPP1R27 ENSG00000288186    116729
## 50337            TBCD ENSG00000278759      6904
## 50344         B3GNTL1 ENSG00000277033    146712
## 50347          METRNL ENSG00000275031    284207
## 50741          CTAGE1 ENSG00000282841     64693
## 51019            CTIF ENSG00000282825      9811
## 51021         MIR4743 ENSG00000282900 100616366
## 51060            SKA1 ENSG00000262634    220134
## 51064           MAPK4 ENSG00000282110      5596
## 51281            DSEL ENSG00000262102     92126
## 51409           SALL3 ENSG00000263310     27164
## 51410           SALL3 ENSG00000277015     27164
## 51412           ATP9B ENSG00000274273    374868
## 51413           ATP9B ENSG00000282266    374868
## 51423           CTDP1 ENSG00000282752      9150
## 51649            MKKS ENSG00000285508      8195
## 51650            MKKS ENSG00000285723      8195
## 51981          COMMD7 ENSG00000285382    149951
## 52222         L3MBTL1 ENSG00000288000     26013
## 52596            CDH4 ENSG00000280641      1002
## 52600            TAF4 ENSG00000280529      6874
## 52667           KCNQ2 ENSG00000281151      3785
## 52713           OPRL1 ENSG00000277044      4987
## 52716          NPBWR2 ENSG00000277339      2832
## 52718            MYT1 ENSG00000276876      4661
## 52720          PCMTD2 ENSG00000280663     55251
## 52781            AZU1 ENSG00000278624       566
## 52783           PRTN3 ENSG00000277804      5657
## 52785           ELANE ENSG00000277571      1991
## 52787             CFD ENSG00000274619      1675
## 52789           MED16 ENSG00000282092     10025
## 52808           SBNO2 ENSG00000278788     22904
## 53217          ZNF177 ENSG00000270011      7730
## 53367          ZNF844 ENSG00000286098    284391
## 53467          ZSWIM4 ENSG00000288360     65249
## 53471         MIR24-2 ENSG00000288126    407013
## 53473          MIR27A ENSG00000288183    407018
## 53475          MIR23A ENSG00000288462    407010
## 53477          NANOS3 ENSG00000288505    342977
## 53479         MIR181C ENSG00000288397    406957
## 53481         MIR181D ENSG00000288329    574457
## 53484          CC2D1A ENSG00000288293     54862
## 53486          PODNL1 ENSG00000288195     79883
## 53488          DCAF15 ENSG00000288453     90379
## 53490            RFX1 ENSG00000288283      5989
## 53492            RLN3 ENSG00000288474    117579
## 53495          IL27RA ENSG00000288185      9466
## 53497           PALM3 ENSG00000288318    342979
## 53501        C19orf67 ENSG00000288239    646457
## 53503           SAMD1 ENSG00000288488     90378
## 53505          PRKACA ENSG00000288516      5566
## 53508           ASF1B ENSG00000288210     55723
## 53716           PDE4C ENSG00000285188      5143
## 53845           ZNF66 ENSG00000275050      7617
## 53850           ZNF85 ENSG00000278091      7639
## 53855          ZNF430 ENSG00000278780     80264
## 53892          ZNF100 ENSG00000274746    163227
## 53898           ZNF43 ENSG00000279566      7594
## 53913          ZNF676 ENSG00000276219    163223
## 53918          ZNF729 ENSG00000279552 100287226
## 54132          LSM14A ENSG00000262860     26065
## 54137             GPI ENSG00000282019      2821
## 54362          MAP4K1 ENSG00000282928     11184
## 54365           EIF3K ENSG00000282986     27335
## 54367           ACTN4 ENSG00000282844        81
## 54372          LGALS7 ENSG00000282902      3963
## 54373          LGALS7 ENSG00000283082      3963
## 54374          LGALS7 ENSG00000178934      3963
## 54376         LGALS7B ENSG00000282902    653499
## 54377         LGALS7B ENSG00000283082    653499
## 54378         LGALS7B ENSG00000205076    653499
## 54381          LGALS4 ENSG00000282992      3960
## 54383            ECH1 ENSG00000282853      1891
## 54387          HNRNPL ENSG00000282947      3191
## 54390            RINL ENSG00000282895    126432
## 54393           SIRT2 ENSG00000283100     22933
## 54395          NFKBIB ENSG00000282905      4793
## 54398           SARS2 ENSG00000283104     54938
## 54401          MRPS12 ENSG00000283018      6183
## 54404          FBXO17 ENSG00000282954    115290
## 54458           LEUTX ENSG00000280774    342900
## 54460          DYRK1B ENSG00000281320      9149
## 54462             FBL ENSG00000280548      2091
## 54464           FCGBP ENSG00000281123      8857
## 54467           PSMC4 ENSG00000281221      5704
## 54469          ZNF546 ENSG00000281526    339327
## 54474         ZNF780B ENSG00000281601    163131
## 54477         ZNF780A ENSG00000280568    284323
## 54554        CEACAM21 ENSG00000278565     90273
## 54558         CEACAM4 ENSG00000274131      1089
## 54563         CEACAM7 ENSG00000280501      1087
## 55311           VSTM1 ENSG00000276159    284415
## 55312           VSTM1 ENSG00000274953    284415
## 55313           VSTM1 ENSG00000275577    284415
## 55314           VSTM1 ENSG00000276363    284415
## 55315           VSTM1 ENSG00000276066    284415
## 55316           VSTM1 ENSG00000277607    284415
## 55317           VSTM1 ENSG00000274887    284415
## 55318           VSTM1 ENSG00000275962    284415
## 55319           VSTM1 ENSG00000275330    284415
## 55321           TARM1 ENSG00000274889    441864
## 55322           TARM1 ENSG00000275123    441864
## 55323           TARM1 ENSG00000275384    441864
## 55324           TARM1 ENSG00000276145    441864
## 55325           TARM1 ENSG00000273875    441864
## 55326           TARM1 ENSG00000277178    441864
## 55327           TARM1 ENSG00000275806    441864
## 55328           TARM1 ENSG00000276604    441864
## 55329           TARM1 ENSG00000276355    441864
## 55331           OSCAR ENSG00000275551    126014
## 55332           OSCAR ENSG00000274703    126014
## 55333           OSCAR ENSG00000275644    126014
## 55334           OSCAR ENSG00000276982    126014
## 55335           OSCAR ENSG00000278378    126014
## 55336           OSCAR ENSG00000278533    126014
## 55337           OSCAR ENSG00000277088    126014
## 55338           OSCAR ENSG00000273511    126014
## 55339           OSCAR ENSG00000275736    126014
## 55341          NDUFA3 ENSG00000275724      4696
## 55342          NDUFA3 ENSG00000278365      4696
## 55343          NDUFA3 ENSG00000276061      4696
## 55344          NDUFA3 ENSG00000276220      4696
## 55345          NDUFA3 ENSG00000273642      4696
## 55346          NDUFA3 ENSG00000277722      4696
## 55347          NDUFA3 ENSG00000276766      4696
## 55348          NDUFA3 ENSG00000275605      4696
## 55349          NDUFA3 ENSG00000274359      4696
## 55351            TFPT ENSG00000276296     29844
## 55352            TFPT ENSG00000273833     29844
## 55353            TFPT ENSG00000276323     29844
## 55354            TFPT ENSG00000276504     29844
## 55355            TFPT ENSG00000275086     29844
## 55356            TFPT ENSG00000276022     29844
## 55357            TFPT ENSG00000276263     29844
## 55358            TFPT ENSG00000278161     29844
## 55359            TFPT ENSG00000274073     29844
## 55361          PRPF31 ENSG00000277953     26121
## 55362          PRPF31 ENSG00000276421     26121
## 55363          PRPF31 ENSG00000275117     26121
## 55364          PRPF31 ENSG00000274894     26121
## 55365          PRPF31 ENSG00000275885     26121
## 55366          PRPF31 ENSG00000274144     26121
## 55367          PRPF31 ENSG00000274651     26121
## 55368          PRPF31 ENSG00000277707     26121
## 55369          PRPF31 ENSG00000277154     26121
## 55372           CNOT3 ENSG00000273943      4849
## 55373           CNOT3 ENSG00000275979      4849
## 55374           CNOT3 ENSG00000274176      4849
## 55375           CNOT3 ENSG00000276082      4849
## 55376           CNOT3 ENSG00000274616      4849
## 55377           CNOT3 ENSG00000277615      4849
## 55378           CNOT3 ENSG00000277114      4849
## 55379           CNOT3 ENSG00000274941      4849
## 55380           CNOT3 ENSG00000277600      4849
## 55382           LENG1 ENSG00000278426     79165
## 55383           LENG1 ENSG00000277457     79165
## 55384           LENG1 ENSG00000276774     79165
## 55385           LENG1 ENSG00000278516     79165
## 55386           LENG1 ENSG00000275935     79165
## 55387           LENG1 ENSG00000278257     79165
## 55388           LENG1 ENSG00000276628     79165
## 55389           LENG1 ENSG00000277808     79165
## 55390           LENG1 ENSG00000276959     79165
## 55392            TMC4 ENSG00000277667    147798
## 55393            TMC4 ENSG00000277996    147798
## 55394            TMC4 ENSG00000276260    147798
## 55395            TMC4 ENSG00000274873    147798
## 55396            TMC4 ENSG00000278363    147798
## 55397            TMC4 ENSG00000274905    147798
## 55398            TMC4 ENSG00000274384    147798
## 55399            TMC4 ENSG00000277789    147798
## 55400            TMC4 ENSG00000273722    147798
## 55402          MBOAT7 ENSG00000277923     79143
## 55403          MBOAT7 ENSG00000277733     79143
## 55404          MBOAT7 ENSG00000275118     79143
## 55405          MBOAT7 ENSG00000278322     79143
## 55406          MBOAT7 ENSG00000277025     79143
## 55407          MBOAT7 ENSG00000274194     79143
## 55408          MBOAT7 ENSG00000278519     79143
## 55409          MBOAT7 ENSG00000273592     79143
## 55410          MBOAT7 ENSG00000276935     79143
## 55412          TSEN34 ENSG00000275165     79042
## 55413          TSEN34 ENSG00000273896     79042
## 55414          TSEN34 ENSG00000274796     79042
## 55415          TSEN34 ENSG00000274672     79042
## 55416          TSEN34 ENSG00000278712     79042
## 55417          TSEN34 ENSG00000274078     79042
## 55418          TSEN34 ENSG00000274129     79042
## 55419          TSEN34 ENSG00000278605     79042
## 55420          TSEN34 ENSG00000278622     79042
## 55424            RPS9 ENSG00000278081      6203
## 55425            RPS9 ENSG00000274005      6203
## 55426            RPS9 ENSG00000278270      6203
## 55427            RPS9 ENSG00000274626      6203
## 55428            RPS9 ENSG00000274646      6203
## 55429            RPS9 ENSG00000275323      6203
## 55430            RPS9 ENSG00000277079      6203
## 55431            RPS9 ENSG00000277359      6203
## 55432            RPS9 ENSG00000274950      6203
## 55435          LILRB3 ENSG00000277816     11025
## 55436          LILRB3 ENSG00000275019     11025
## 55437          LILRB3 ENSG00000274587     11025
## 55439          LILRA6 ENSG00000275539     79168
## 55440          LILRA6 ENSG00000277177     79168
## 55441          LILRA6 ENSG00000275584     79168
## 55442          LILRA6 ENSG00000274148     79168
## 55448          LILRB5 ENSG00000273991     10990
## 55449          LILRB5 ENSG00000274311     10990
## 55450          LILRB5 ENSG00000277414     10990
## 55451          LILRB5 ENSG00000278437     10990
## 55456          LILRB2 ENSG00000274513     10288
## 55457          LILRB2 ENSG00000277751     10288
## 55458          LILRB2 ENSG00000275463     10288
## 55459          LILRB2 ENSG00000276146     10288
## 55463          LILRA3 ENSG00000278046     11026
## 55464          LILRA3 ENSG00000276175     11026
## 55465          LILRA3 ENSG00000275841     11026
## 55469          LILRA5 ENSG00000278355    353514
## 55470          LILRA5 ENSG00000275404    353514
## 55471          LILRA5 ENSG00000274914    353514
## 55472          LILRA5 ENSG00000274113    353514
## 55477          LILRA4 ENSG00000276798     23547
## 55478          LILRA4 ENSG00000274185     23547
## 55479          LILRA4 ENSG00000277092     23547
## 55482           LAIR1 ENSG00000276163      3903
## 55483           LAIR1 ENSG00000278154      3903
## 55484           LAIR1 ENSG00000274110      3903
## 55485           LAIR1 ENSG00000276053      3903
## 55488           TTYH1 ENSG00000276887     57348
## 55489           TTYH1 ENSG00000276537     57348
## 55490           TTYH1 ENSG00000275650     57348
## 55496       LENG8-AS1 ENSG00000275470 104355426
## 55499           LENG8 ENSG00000274305    114823
## 55500           LENG8 ENSG00000276458    114823
## 55501           LENG8 ENSG00000276681    114823
## 55503           LENG9 ENSG00000274495     94059
## 55504           LENG9 ENSG00000278312     94059
## 55505           LENG9 ENSG00000273574     94059
## 55507        CDC42EP5 ENSG00000273622    148170
## 55508        CDC42EP5 ENSG00000273633    148170
## 55509        CDC42EP5 ENSG00000278444    148170
## 55511           LAIR2 ENSG00000274084      3904
## 55512           LAIR2 ENSG00000275819      3904
## 55513           LAIR2 ENSG00000277335      3904
## 55518          LILRA2 ENSG00000278634     11027
## 55519          LILRA2 ENSG00000274000     11027
## 55520          LILRA2 ENSG00000275290     11027
## 55522          LILRB1 ENSG00000277807     10859
## 55523          LILRB1 ENSG00000276452     10859
## 55524          LILRB1 ENSG00000274669     10859
## 55525          LILRB1 ENSG00000277134     10859
## 55528          LILRA1 ENSG00000277398     11024
## 55529          LILRA1 ENSG00000274935     11024
## 55530          LILRA1 ENSG00000275525     11024
## 55535          LILRB4 ENSG00000278555     11006
## 55536          LILRB4 ENSG00000278279     11006
## 55537          LILRB4 ENSG00000276042     11006
## 55538          LILRB4 ENSG00000275730     11006
## 55546          LILRP2 ENSG00000274826     79166
## 55547          LILRP2 ENSG00000273755     79166
## 55548          LILRP2 ENSG00000275442     79166
## 55549          LILRP2 ENSG00000274861     79166
## 55550          LILRP2 ENSG00000274120     79166
## 55551          LILRP2 ENSG00000276247     79166
## 55552          LILRP2 ENSG00000277267     79166
## 55553          LILRP2 ENSG00000275289     79166
## 55554          LILRP2 ENSG00000277963     79166
## 55555          LILRP2 ENSG00000274788     79166
## 55556          LILRP2 ENSG00000276243     79166
## 55557          LILRP2 ENSG00000278288     79166
## 55558          LILRP2 ENSG00000274842     79166
## 55559          LILRP2 ENSG00000273883     79166
## 55560          LILRP2 ENSG00000277271     79166
## 55561          LILRP2 ENSG00000273528     79166
## 55562          LILRP2 ENSG00000276512     79166
## 55563          LILRP2 ENSG00000273922     79166
## 55564          LILRP2 ENSG00000273666     79166
## 55565          LILRP2 ENSG00000275462     79166
## 55566          LILRP2 ENSG00000278795     79166
## 55567          LILRP2 ENSG00000276976     79166
## 55568          LILRP2 ENSG00000273864     79166
## 55569          LILRP2 ENSG00000284141     79166
## 55570          LILRP2 ENSG00000283942     79166
## 55571          LILRP2 ENSG00000283800     79166
## 55572          LILRP2 ENSG00000283794     79166
## 55573          LILRP2 ENSG00000284051     79166
## 55574          LILRP2 ENSG00000283983     79166
## 55575          LILRP2 ENSG00000283732     79166
## 55576          LILRP2 ENSG00000284405     79166
## 55577          LILRP2 ENSG00000284097     79166
## 55578          LILRP2 ENSG00000284374     79166
## 55579          LILRP2 ENSG00000284339     79166
## 55580          LILRP2 ENSG00000284030     79166
## 55581          LILRP2 ENSG00000284314     79166
## 55582          LILRP2 ENSG00000284593     79166
## 55584         KIR3DL1 ENSG00000276379      3811
## 55585         KIR3DL1 ENSG00000276501      3811
## 55586         KIR3DL1 ENSG00000273775      3811
## 55587         KIR3DL1 ENSG00000277272      3811
## 55588         KIR3DL1 ENSG00000275717      3811
## 55589         KIR3DL1 ENSG00000274146      3811
## 55590         KIR3DL1 ENSG00000276329      3811
## 55591         KIR3DL1 ENSG00000275786      3811
## 55592         KIR3DL1 ENSG00000275288      3811
## 55593         KIR3DL1 ENSG00000274948      3811
## 55594         KIR3DL1 ENSG00000276423      3811
## 55595         KIR3DL1 ENSG00000278856      3811
## 55596         KIR3DL1 ENSG00000275659      3811
## 55597         KIR3DL1 ENSG00000274920      3811
## 55598         KIR3DL1 ENSG00000278079      3811
## 55599         KIR3DL1 ENSG00000278368      3811
## 55600         KIR3DL1 ENSG00000273518      3811
## 55601         KIR3DL1 ENSG00000278427      3811
## 55602         KIR3DL1 ENSG00000275486      3811
## 55603         KIR3DL1 ENSG00000277175      3811
## 55604         KIR3DL1 ENSG00000274036      3811
## 55605         KIR3DL1 ENSG00000275545      3811
## 55606         KIR3DL1 ENSG00000284177      3811
## 55607         KIR3DL1 ENSG00000283954      3811
## 55608         KIR3DL1 ENSG00000284342      3811
## 55609         KIR3DL1 ENSG00000284426      3811
## 55610         KIR3DL1 ENSG00000283731      3811
## 55611         KIR3DL1 ENSG00000283729      3811
## 55612         KIR3DL1 ENSG00000284093      3811
## 55613         KIR3DL1 ENSG00000284589      3811
## 55614         KIR3DL1 ENSG00000283827      3811
## 55616         KIR3DL3 ENSG00000277620    115653
## 55617         KIR3DL3 ENSG00000276433    115653
## 55618         KIR3DL3 ENSG00000274696    115653
## 55619         KIR3DL3 ENSG00000276930    115653
## 55620         KIR3DL3 ENSG00000275172    115653
## 55621         KIR3DL3 ENSG00000274639    115653
## 55622         KIR3DL3 ENSG00000274724    115653
## 55623         KIR3DL3 ENSG00000278490    115653
## 55624         KIR3DL3 ENSG00000273502    115653
## 55625         KIR3DL3 ENSG00000275433    115653
## 55626         KIR3DL3 ENSG00000276806    115653
## 55627         KIR3DL3 ENSG00000274480    115653
## 55628         KIR3DL3 ENSG00000274556    115653
## 55629         KIR3DL3 ENSG00000277552    115653
## 55630         KIR3DL3 ENSG00000274786    115653
## 55631         KIR3DL3 ENSG00000277392    115653
## 55632         KIR3DL3 ENSG00000277596    115653
## 55633         KIR3DL3 ENSG00000277028    115653
## 55634         KIR3DL3 ENSG00000275062    115653
## 55635         KIR3DL3 ENSG00000275513    115653
## 55636         KIR3DL3 ENSG00000276328    115653
## 55637         KIR3DL3 ENSG00000276084    115653
## 55638         KIR3DL3 ENSG00000274763    115653
## 55639         KIR3DL3 ENSG00000274254    115653
## 55640         KIR3DL3 ENSG00000276086    115653
## 55641         KIR3DL3 ENSG00000276572    115653
## 55642         KIR3DL3 ENSG00000274394    115653
## 55643         KIR3DL3 ENSG00000274511    115653
## 55644         KIR3DL3 ENSG00000276875    115653
## 55645         KIR3DL3 ENSG00000278729    115653
## 55646         KIR3DL3 ENSG00000276196    115653
## 55647         KIR3DL3 ENSG00000278723    115653
## 55648         KIR3DL3 ENSG00000283823    115653
## 55649         KIR3DL3 ENSG00000284104    115653
## 55650         KIR3DL3 ENSG00000284086    115653
## 55651         KIR3DL3 ENSG00000283875    115653
## 55652         KIR3DL3 ENSG00000283915    115653
## 55653         KIR3DL3 ENSG00000283966    115653
## 55654         KIR3DL3 ENSG00000284127    115653
## 55655         KIR3DL3 ENSG00000284480    115653
## 55656         KIR3DL3 ENSG00000284371    115653
## 55659         KIR2DL4 ENSG00000277355      3805
## 55660         KIR2DL4 ENSG00000275699      3805
## 55661         KIR2DL4 ENSG00000274189      3805
## 55662         KIR2DL4 ENSG00000275732      3805
## 55663         KIR2DL4 ENSG00000273575      3805
## 55664         KIR2DL4 ENSG00000274945      3805
## 55665         KIR2DL4 ENSG00000276779      3805
## 55666         KIR2DL4 ENSG00000274955      3805
## 55667         KIR2DL4 ENSG00000275237      3805
## 55668         KIR2DL4 ENSG00000276044      3805
## 55669         KIR2DL4 ENSG00000277964      3805
## 55670         KIR2DL4 ENSG00000275848      3805
## 55671         KIR2DL4 ENSG00000277076      3805
## 55672         KIR2DL4 ENSG00000277362      3805
## 55673         KIR2DL4 ENSG00000274193      3805
## 55674         KIR2DL4 ENSG00000277750      3805
## 55675         KIR2DL4 ENSG00000275456      3805
## 55676         KIR2DL4 ENSG00000277850      3805
## 55677         KIR2DL4 ENSG00000278074      3805
## 55678         KIR2DL4 ENSG00000275317      3805
## 55679         KIR2DL4 ENSG00000278430      3805
## 55680         KIR2DL4 ENSG00000278606      3805
## 55681         KIR2DL4 ENSG00000278201      3805
## 55682         KIR2DL4 ENSG00000278271      3805
## 55683         KIR2DL4 ENSG00000273498      3805
## 55684         KIR2DL4 ENSG00000277540      3805
## 55685         KIR2DL4 ENSG00000276979      3805
## 55686         KIR2DL4 ENSG00000274609      3805
## 55687         KIR2DL4 ENSG00000274232      3805
## 55688         KIR2DL4 ENSG00000284509      3805
## 55689         KIR2DL4 ENSG00000283961      3805
## 55690         KIR2DL4 ENSG00000284457      3805
## 55691         KIR2DL4 ENSG00000284013      3805
## 55692         KIR2DL4 ENSG00000284365      3805
## 55693         KIR2DL4 ENSG00000283869      3805
## 55694         KIR2DL4 ENSG00000283986      3805
## 55695         KIR2DL4 ENSG00000284340      3805
## 55696         KIR2DL4 ENSG00000284562      3805
## 55697         KIR2DL4 ENSG00000284206      3805
## 55698         KIR2DL4 ENSG00000284460      3805
## 55700         KIR2DL3 ENSG00000276459      3804
## 55701         KIR2DL3 ENSG00000277484      3804
## 55702         KIR2DL3 ENSG00000277317      3804
## 55703         KIR2DL3 ENSG00000273947      3804
## 55704         KIR2DL3 ENSG00000274830      3804
## 55705         KIR2DL3 ENSG00000276590      3804
## 55706         KIR2DL3 ENSG00000276218      3804
## 55707         KIR2DL3 ENSG00000274108      3804
## 55708         KIR2DL3 ENSG00000278369      3804
## 55709         KIR2DL3 ENSG00000278327      3804
## 55710         KIR2DL3 ENSG00000273887      3804
## 55711         KIR2DL3 ENSG00000277554      3804
## 55712         KIR2DL3 ENSG00000275008      3804
## 55713         KIR2DL3 ENSG00000274402      3804
## 55714         KIR2DL3 ENSG00000275623      3804
## 55715         KIR2DL3 ENSG00000275658      3804
## 55716         KIR2DL3 ENSG00000277924      3804
## 55717         KIR2DL3 ENSG00000274952      3804
## 55718         KIR2DL3 ENSG00000274410      3804
## 55719         KIR2DL3 ENSG00000283996      3804
## 55720         KIR2DL3 ENSG00000284504      3804
## 55721         KIR2DL3 ENSG00000283702      3804
## 55722         KIR2DL3 ENSG00000284132      3804
## 55723         KIR2DL3 ENSG00000284044      3804
## 55724         KIR2DL3 ENSG00000283708      3804
## 55725         KIR2DL3 ENSG00000283790      3804
## 55726         KIR2DL3 ENSG00000284241      3804
## 55727         KIR2DL3 ENSG00000284510      3804
## 55728         KIR2DL3 ENSG00000284236      3804
## 55729         KIR2DL3 ENSG00000284333      3804
## 55732         KIR2DL1 ENSG00000277616      3802
## 55733         KIR2DL1 ENSG00000278805      3802
## 55734         KIR2DL1 ENSG00000278248      3802
## 55735         KIR2DL1 ENSG00000276820      3802
## 55736         KIR2DL1 ENSG00000274782      3802
## 55737         KIR2DL1 ENSG00000278207      3802
## 55738         KIR2DL1 ENSG00000273510      3802
## 55739         KIR2DL1 ENSG00000278755      3802
## 55740         KIR2DL1 ENSG00000275750      3802
## 55741         KIR2DL1 ENSG00000275080      3802
## 55742         KIR2DL1 ENSG00000277356      3802
## 55743         KIR2DL1 ENSG00000276310      3802
## 55744         KIR2DL1 ENSG00000273794      3802
## 55745         KIR2DL1 ENSG00000278495      3802
## 55746         KIR2DL1 ENSG00000274692      3802
## 55747         KIR2DL1 ENSG00000276625      3802
## 55748         KIR2DL1 ENSG00000275276      3802
## 55749         KIR2DL1 ENSG00000278821      3802
## 55750         KIR2DL1 ENSG00000277833      3802
## 55751         KIR2DL1 ENSG00000276387      3802
## 55752         KIR2DL1 ENSG00000275522      3802
## 55753         KIR2DL1 ENSG00000275196      3802
## 55754         KIR2DL1 ENSG00000274926      3802
## 55755         KIR2DL1 ENSG00000278738      3802
## 55756         KIR2DL1 ENSG00000278503      3802
## 55757         KIR2DL1 ENSG00000284530      3802
## 55758         KIR2DL1 ENSG00000283723      3802
## 55759         KIR2DL1 ENSG00000284514      3802
## 55760         KIR2DL1 ENSG00000284145      3802
## 55761         KIR2DL1 ENSG00000284100      3802
## 55762         KIR2DL1 ENSG00000284401      3802
## 55763         KIR2DL1 ENSG00000284551      3802
## 55764         KIR2DL1 ENSG00000284347      3802
## 55767         KIR2DS4 ENSG00000274324      3809
## 55768         KIR2DS4 ENSG00000277345      3809
## 55769         KIR2DS4 ENSG00000274807      3809
## 55770         KIR2DS4 ENSG00000275938      3809
## 55771         KIR2DS4 ENSG00000274714      3809
## 55772         KIR2DS4 ENSG00000276885      3809
## 55773         KIR2DS4 ENSG00000276154      3809
## 55774         KIR2DS4 ENSG00000277078      3809
## 55775         KIR2DS4 ENSG00000273526      3809
## 55776         KIR2DS4 ENSG00000276395      3809
## 55777         KIR2DS4 ENSG00000274947      3809
## 55778         KIR2DS4 ENSG00000276465      3809
## 55779         KIR2DS4 ENSG00000276209      3809
## 55780         KIR2DS4 ENSG00000275353      3809
## 55781         KIR2DS4 ENSG00000274957      3809
## 55782         KIR2DS4 ENSG00000276254      3809
## 55783         KIR2DS4 ENSG00000274406      3809
## 55784         KIR2DS4 ENSG00000275351      3809
## 55785         KIR2DS4 ENSG00000275731      3809
## 55786         KIR2DS4 ENSG00000274533      3809
## 55787         KIR2DS4 ENSG00000274921      3809
## 55788         KIR2DS4 ENSG00000276634      3809
## 55789         KIR2DS4 ENSG00000273931      3809
## 55790         KIR2DS4 ENSG00000284408      3809
## 55791         KIR2DS4 ENSG00000284307      3809
## 55792         KIR2DS4 ENSG00000283727      3809
## 55793         KIR2DS4 ENSG00000284244      3809
## 55794         KIR2DS4 ENSG00000283779      3809
## 55795         KIR2DS4 ENSG00000283870      3809
## 55796         KIR2DS4 ENSG00000283882      3809
## 55797         KIR2DS4 ENSG00000284264      3809
## 55798         KIR2DS4 ENSG00000283846      3809
## 55800         KIR3DL2 ENSG00000276424      3812
## 55801         KIR3DL2 ENSG00000273735      3812
## 55802         KIR3DL2 ENSG00000276357      3812
## 55803         KIR3DL2 ENSG00000278850      3812
## 55804         KIR3DL2 ENSG00000278710      3812
## 55805         KIR3DL2 ENSG00000274722      3812
## 55806         KIR3DL2 ENSG00000276004      3812
## 55807         KIR3DL2 ENSG00000278758      3812
## 55808         KIR3DL2 ENSG00000278726      3812
## 55809         KIR3DL2 ENSG00000278442      3812
## 55810         KIR3DL2 ENSG00000278474      3812
## 55811         KIR3DL2 ENSG00000278656      3812
## 55812         KIR3DL2 ENSG00000275629      3812
## 55813         KIR3DL2 ENSG00000276882      3812
## 55814         KIR3DL2 ENSG00000275416      3812
## 55815         KIR3DL2 ENSG00000278809      3812
## 55816         KIR3DL2 ENSG00000277982      3812
## 55817         KIR3DL2 ENSG00000278361      3812
## 55818         KIR3DL2 ENSG00000275262      3812
## 55819         KIR3DL2 ENSG00000275083      3812
## 55820         KIR3DL2 ENSG00000275626      3812
## 55821         KIR3DL2 ENSG00000275511      3812
## 55822         KIR3DL2 ENSG00000278403      3812
## 55823         KIR3DL2 ENSG00000275838      3812
## 55824         KIR3DL2 ENSG00000276739      3812
## 55825         KIR3DL2 ENSG00000278707      3812
## 55826         KIR3DL2 ENSG00000277709      3812
## 55827         KIR3DL2 ENSG00000275566      3812
## 55828         KIR3DL2 ENSG00000273911      3812
## 55829         KIR3DL2 ENSG00000277181      3812
## 55830         KIR3DL2 ENSG00000284063      3812
## 55831         KIR3DL2 ENSG00000288389      3812
## 55832         KIR3DL2 ENSG00000284384      3812
## 55833         KIR3DL2 ENSG00000284295      3812
## 55834         KIR3DL2 ENSG00000284381      3812
## 55835         KIR3DL2 ENSG00000283975      3812
## 55836         KIR3DL2 ENSG00000284213      3812
## 55837         KIR3DL2 ENSG00000284528      3812
## 55838         KIR3DL2 ENSG00000284192      3812
## 55839         KIR3DL2 ENSG00000284466      3812
## 55840         KIR3DL2 ENSG00000284046      3812
## 55841         KIR3DL2 ENSG00000283951      3812
## 55844            FCAR ENSG00000276858      2204
## 55845            FCAR ENSG00000276985      2204
## 55846            FCAR ENSG00000273738      2204
## 55847            FCAR ENSG00000275136      2204
## 55848            FCAR ENSG00000275970      2204
## 55849            FCAR ENSG00000275269      2204
## 55850            FCAR ENSG00000278415      2204
## 55851            FCAR ENSG00000275564      2204
## 55852            FCAR ENSG00000274580      2204
## 55853            FCAR ENSG00000283953      2204
## 55854            FCAR ENSG00000284004      2204
## 55855            FCAR ENSG00000284245      2204
## 55856            FCAR ENSG00000284061      2204
## 55857            FCAR ENSG00000283750      2204
## 55860            NCR1 ENSG00000277334      9437
## 55861            NCR1 ENSG00000275521      9437
## 55862            NCR1 ENSG00000276450      9437
## 55863            NCR1 ENSG00000278025      9437
## 55864            NCR1 ENSG00000277442      9437
## 55865            NCR1 ENSG00000275637      9437
## 55866            NCR1 ENSG00000278362      9437
## 55867            NCR1 ENSG00000277824      9437
## 55868            NCR1 ENSG00000273916      9437
## 55869            NCR1 ENSG00000277629      9437
## 55870            NCR1 ENSG00000273535      9437
## 55871            NCR1 ENSG00000274053      9437
## 55872            NCR1 ENSG00000273506      9437
## 55873            NCR1 ENSG00000275822      9437
## 55874            NCR1 ENSG00000275156      9437
## 55875            NCR1 ENSG00000288651      9437
## 55876            NCR1 ENSG00000284113      9437
## 55878           NLRP7 ENSG00000277071    199713
## 55879           NLRP7 ENSG00000277776    199713
## 55880           NLRP7 ENSG00000274174    199713
## 55881           NLRP7 ENSG00000276804    199713
## 55882           NLRP7 ENSG00000274571    199713
## 55883           NLRP7 ENSG00000278173    199713
## 55884           NLRP7 ENSG00000275483    199713
## 55885           NLRP7 ENSG00000277179    199713
## 55886           NLRP7 ENSG00000277786    199713
## 55889           NLRP2 ENSG00000275399     55655
## 55890           NLRP2 ENSG00000278789     55655
## 55891           NLRP2 ENSG00000275796     55655
## 55892           NLRP2 ENSG00000275843     55655
## 55893           NLRP2 ENSG00000277060     55655
## 55894           NLRP2 ENSG00000278682     55655
## 55895           NLRP2 ENSG00000273992     55655
## 55896           NLRP2 ENSG00000274638     55655
## 55897           NLRP2 ENSG00000275082     55655
## 55901             GP6 ENSG00000274566     51206
## 55902             GP6 ENSG00000274050     51206
## 55903             GP6 ENSG00000275633     51206
## 55904             GP6 ENSG00000276065     51206
## 55905             GP6 ENSG00000277439     51206
## 55906             GP6 ENSG00000275931     51206
## 55907             GP6 ENSG00000278670     51206
## 55908             GP6 ENSG00000278316     51206
## 55909             GP6 ENSG00000276211     51206
## 55912           RDH13 ENSG00000275474    112724
## 55913           RDH13 ENSG00000274504    112724
## 55914           RDH13 ENSG00000276826    112724
## 55915           RDH13 ENSG00000273944    112724
## 55916           RDH13 ENSG00000278284    112724
## 55917           RDH13 ENSG00000276341    112724
## 55918           RDH13 ENSG00000276684    112724
## 55919           RDH13 ENSG00000274418    112724
## 55920           RDH13 ENSG00000278149    112724
## 56125          ZNF544 ENSG00000283515     27300
## 56487          TTTY13 ENSG00000285001     83868
## 56605         TTTY17C ENSG00000227439    474152
## 57009         ZNF280B ENSG00000277421    140883
## 57011         ZNF280A ENSG00000275499    129025
## 57013           PRAME ENSG00000275013     23532
## 57015 LL22NC03-63E9.3 ENSG00000281296    648691
## 57117        C22orf15 ENSG00000273579    150248
## 57119         CHCHD10 ENSG00000273607    400916
## 57121           MMP11 ENSG00000275365      4320
## 57124         SMARCB1 ENSG00000275837      6598
## 57126           DERL3 ENSG00000274437     91319
## 57129         SLC2A11 ENSG00000275744     66035
## 57133             MIF ENSG00000276701      4282
## 57140          GSTT2B ENSG00000278695    653689
## 57143            DDTL ENSG00000275003 100037417
## 57144            DDTL ENSG00000275758 100037417
## 57145            DDTL ENSG00000099977 100037417
## 57148             DDT ENSG00000285762      1652
## 57149             DDT ENSG00000275003      1652
## 57152           GSTT2 ENSG00000277897      2953
## 57165          CABIN1 ENSG00000281670     23523
## 57182            GGT1 ENSG00000286070      2678
## 57469           APOL5 ENSG00000277390     80831
## 57471          RBFOX2 ENSG00000277564     23543
## 57499           PVALB ENSG00000274665      5816
## 57503            NCF4 ENSG00000275990      4689
## 57526           ELFN2 ENSG00000243902    114794
## 57600        APOBEC3A ENSG00000262156    200315
## 57603    APOBEC3B-AS1 ENSG00000262679 100874530
## 57625           MIEF1 ENSG00000285025     54471
## 57710           SMDT1 ENSG00000272835     91689
## 57711           SMDT1 ENSG00000272901     91689
## 57712           SMDT1 ENSG00000274112     91689
## 57714          NDUFA6 ENSG00000273397      4700
## 57715          NDUFA6 ENSG00000272765      4700
## 57716          NDUFA6 ENSG00000277365      4700
## 57717          NDUFA6 ENSG00000281013      4700
## 57722          CYP2D6 ENSG00000272532      1565
## 57723          CYP2D6 ENSG00000275211      1565
## 57724          CYP2D6 ENSG00000280905      1565
## 57725          CYP2D6 ENSG00000282966      1565
## 57726          CYP2D6 ENSG00000283284      1565
## 57732           TCF20 ENSG00000262024      6942
## 57733           TCF20 ENSG00000276461      6942
## 57734           TCF20 ENSG00000281897      6942
## 57735           TCF20 ENSG00000280467      6942
## 57736           TCF20 ENSG00000283026      6942
## 57737           TCF20 ENSG00000282892      6942
## 57738           TCF20 ENSG00000283681      6942
## 57932             ACR ENSG00000283539        49
## 58045            BTG3 ENSG00000281484     10950
## 58093       LINC00308 ENSG00000262510     54143
## 58280          PAXBP1 ENSG00000263141     94104
## 58283        C21orf62 ENSG00000262938     56245
## 58295          IFNAR2 ENSG00000249624      3455
## 58303          IFNGR2 ENSG00000262795      3460
## 58305         TMEM50B ENSG00000263160       757
## 58310         DNAJC28 ENSG00000262911     54943
## 58312            GART ENSG00000262473      2618
## 58632            FTCD ENSG00000281775     10841
## 58634        FTCD-AS1 ENSG00000280541 100861507
## 58636         SPATC1L ENSG00000274679     84221
## 58639             LSS ENSG00000281289      4047
## 58747        HLA-DRB4 ENSG00000231021      3126
## 58748        HLA-DRB4 ENSG00000227826      3126
## 58987        HLA-DRB3 ENSG00000196101      3125
## 58988        HLA-DRB3 ENSG00000231679      3125
## 59183           PRSS2 ENSG00000282049      5645
## 59188         KIR2DS2 ENSG00000274518 100132285
## 59189         KIR2DS2 ENSG00000276139 100132285
## 59190         KIR2DS2 ENSG00000276425 100132285
## 59191         KIR2DS2 ENSG00000278152 100132285
## 59192         KIR2DS2 ENSG00000277885 100132285
## 59193         KIR2DS2 ENSG00000275452 100132285
## 59194         KIR2DS2 ENSG00000274438 100132285
## 59195         KIR2DS2 ENSG00000275253 100132285
## 59196         KIR2DS2 ENSG00000275735 100132285
## 59197         KIR2DS2 ENSG00000275737 100132285
## 59198         KIR2DS2 ENSG00000278300 100132285
## 59199         KIR2DS2 ENSG00000275583 100132285
## 59235         KIR2DS1 ENSG00000273517      3806
## 59236         KIR2DS1 ENSG00000276327      3806
## 59237         KIR2DS1 ENSG00000278304      3806
## 59238         KIR2DS1 ENSG00000273603      3806
## 59239         KIR2DS1 ENSG00000275306      3806
## 59240         KIR2DS1 ENSG00000278120      3806
## 59241         KIR2DS1 ENSG00000275921      3806
## 59242         KIR2DS1 ENSG00000284150      3806
## 59243         KIR2DS1 ENSG00000284560      3806
## 59244         KIR2DS1 ENSG00000284120      3806
## 59245         KIR2DS1 ENSG00000283937      3806
## 59247         KIR2DL2 ENSG00000275407      3803
## 59248         KIR2DL2 ENSG00000275914      3803
## 59249         KIR2DL2 ENSG00000273578      3803
## 59250         KIR2DL2 ENSG00000277725      3803
## 59251         KIR2DL2 ENSG00000273661      3803
## 59252         KIR2DL2 ENSG00000276011      3803
## 59253         KIR2DL2 ENSG00000275546      3803
## 59254         KIR2DL2 ENSG00000277251      3803
## 59255         KIR2DL2 ENSG00000278692      3803
## 59256         KIR2DL2 ENSG00000276731      3803
## 59257         KIR2DL2 ENSG00000275960      3803
## 59258         KIR2DL2 ENSG00000274412      3803
## 59262         KIR2DS5 ENSG00000274243      3810
## 59263         KIR2DS5 ENSG00000277650      3810
## 59264         KIR2DS5 ENSG00000274563      3810
## 59265         KIR2DS5 ENSG00000275047      3810
## 59266         KIR2DS5 ENSG00000274739      3810
## 59267         KIR2DS5 ENSG00000284217      3810
## 59268         KIR2DS5 ENSG00000288206      3810
## 59269         KIR2DS5 ENSG00000288357      3810
##                                                                                                                         GENENAME
## 170                                                                                                        phospholipase C eta 2
## 174                                                                                             pantothenate kinase 4 (inactive)
## 176                                                                                       hes family bHLH transcription factor 5
## 180                                                                                           TNF receptor superfamily member 14
## 185                                                                                         membrane metalloendopeptidase like 1
## 188                                                                                           tetratricopeptide repeat domain 34
## 426                                                                                                       PRAME family member 11
## 429                                                                             heterogeneous nuclear ribonucleoprotein C like 1
## 431                                                                                                        PRAME family member 2
## 433                                                                                                        PRAME family member 4
## 435                                                                                                       PRAME family member 10
## 437                                                                                                        PRAME family member 7
## 441                                                                                                        PRAME family member 6
## 448                                                                                                       PRAME family member 25
## 449                                                                                                       PRAME family member 25
## 450                                                                                                       PRAME family member 25
## 457                                                                                                       PRAME family member 26
## 458                                                                                                       PRAME family member 26
## 459                                                                                                       PRAME family member 26
## 460                                                                                                       PRAME family member 26
## 461                                                                                                       PRAME family member 26
## 462                                                                                                       PRAME family member 26
## 466                                                                                                        PRAME family member 5
## 467                                                                                                        PRAME family member 5
## 468                                                                                                        PRAME family member 5
## 472                                                                                                        PRAME family member 8
## 473                                                                                                        PRAME family member 8
## 474                                                                                                        PRAME family member 8
## 477                                                                                                        PRAME family member 9
## 478                                                                                                        PRAME family member 9
## 479                                                                                                        PRAME family member 9
## 482                                                                                                       PRAME family member 13
## 484                                                                                                       PRAME family member 18
## 485                                                                                                       PRAME family member 18
## 608                                                                                                peptidyl arginine deiminase 1
## 610                                                                                                peptidyl arginine deiminase 3
## 612                                                                                                                microRNA 3972
## 614                                                                                                peptidyl arginine deiminase 4
## 617                                                                                                peptidyl arginine deiminase 6
## 620                                                                                       regulator of chromosome condensation 2
## 765                                                                                    heterogeneous nuclear ribonucleoprotein R
## 767                                                                                                      zinc finger protein 436
## 771                                                                                           transcription elongation factor A3
## 774                                                                       ArfGAP with SH3 domain, ankyrin repeat and PH domain 3
## 776                                                                                                   E2F transcription factor 2
## 779                                                                                      inhibitor of DNA binding 3, HLH protein
## 890                                                                                               ribosomal protein S6 kinase A1
## 892                                                                                                                microRNA 1976
## 968                                                                             DnaJ heat shock protein family (Hsp40) member C8
## 975                                                                                                                    sestrin 2
## 977                                                                                                  mediator complex subunit 18
## 1320                                                                                                             forkhead box O6
## 2433                                                                                                        VAV3 antisense RNA 1
## 2437                                                                                          solute carrier family 25 member 24
## 2597                                                                                           solute carrier family 16 member 1
## 2971                                                                                          peptidylprolyl isomerase A like 4F
## 3247                                                                                                integrator complex subunit 3
## 3251                                                                                           solute carrier family 27 member 3
## 3254                                                                                       GATA zinc finger domain containing 2B
## 3334                                                                                                     glucosylceramidase beta
## 3337                                                                                family with sequence similarity 189 member B
## 3339                                                                                        secretory carrier membrane protein 3
## 3341                                                                                                           CDC like kinase 2
## 3343                                                     hyperpolarization activated cyclic nucleotide gated potassium channel 3
## 3345                                                                                                         pyruvate kinase L/R
## 3659                                                                                          regulator of G protein signaling 5
## 3932                                                                        SEC16 homolog B, endoplasmic reticulum export factor
## 3977                                                                                family with sequence similarity 163 member A
## 4210                                                                                        ATPase H+ transporting V1 subunit G3
## 4213                                                                                protein tyrosine phosphatase receptor type C
## 4498                                                                                                   SERTA domain containing 4
## 4502                                                                                                    hedgehog acyltransferase
## 4819                                                                                              tripartite motif containing 17
## 4825                                                                                                              microRNA 4666a
## 4828                                                                                                     ring finger protein 187
## 4833                                                                                                         RNA, 5S ribosomal 1
## 4835                                                                                                         RNA, 5S ribosomal 2
## 4837                                                                                                         RNA, 5S ribosomal 3
## 4847                                                                                                        RNA, 5S ribosomal 12
## 4848                                                                                                        RNA, 5S ribosomal 12
## 4853                                                                                                        RNA, 5S ribosomal 16
## 4855                                                                                                        RNA, 5S ribosomal 17
## 4859                                                                                                 ras homolog family member U
## 4995                                                                                                  tubulin folding cofactor E
## 4996                                                                                                  tubulin folding cofactor E
## 5000                                                                                beta-1,3-N-acetylgalactosaminyltransferase 2
## 5009                                                                                                   G protein subunit gamma 4
## 5091                                                                                                                     opsin 3
## 5121                                                                                                     centrosomal protein 170
## 5126                                                                            SHH signaling and ciliogenesis regulator SDCCAG8
## 5130                                                                                               AKT serine/threonine kinase 3
## 5163                                                                                                   kinesin family member 26B
## 5261                                                                            olfactory receptor family 2 subfamily T member 4
## 5262                                                                            olfactory receptor family 2 subfamily T member 4
## 5264                                                                            olfactory receptor family 2 subfamily T member 6
## 5265                                                                            olfactory receptor family 2 subfamily T member 6
## 5267                                                                            olfactory receptor family 2 subfamily T member 1
## 5268                                                                            olfactory receptor family 2 subfamily T member 1
## 5270                                                                            olfactory receptor family 2 subfamily T member 7
## 5271                                                                            olfactory receptor family 2 subfamily T member 7
## 5273                                                                            olfactory receptor family 2 subfamily T member 2
## 5274                                                                            olfactory receptor family 2 subfamily T member 2
## 5276                                                                            olfactory receptor family 2 subfamily T member 3
## 5277                                                                            olfactory receptor family 2 subfamily T member 3
## 5280                                                                            olfactory receptor family 2 subfamily T member 5
## 5281                                                                            olfactory receptor family 2 subfamily T member 5
## 5332                                                                                                          syntrophin gamma 2
## 5333                                                                                                          syntrophin gamma 2
## 5338                                                                                                          thyroid peroxidase
## 5357                                                                             trafficking protein particle complex subunit 12
## 5361                                                                                                  acireductone dioxygenase 1
## 5831                                                                                                 mediator of cell motility 1
## 5850                                                                                  long intergenic non-protein coding RNA 486
## 5883                                                                                 cysteine rich transmembrane BMP regulator 1
## 6400                                                                                        aspartic peptidase retroviral like 1
## 6862                                                                                                         ACTR3B pseudogene 2
## 7308                                                                                         ribosomal protein L23a pseudogene 7
## 7765                                                                                                    kinesin family member 5C
## 7883                                                                               bromodomain adjacent to zinc finger domain 2B
## 7983                                                                                           nitric oxide synthase trafficking
## 7985                                                                                SPC25 component of NDC80 kinetochore complex
## 7987                                                                                   glucose-6-phosphatase catalytic subunit 2
## 7989                                                                                  ATP binding cassette subfamily B member 11
## 8021                                                                                                            glutamate rich 2
## 8546                                                                                                     INO80 complex subunit D
## 8550                                                                              NADH:ubiquinone oxidoreductase core subunit S1
## 8554                                                                           eukaryotic translation elongation factor 1 beta 2
## 8557                                                                                           small nucleolar RNA, H/ACA box 41
## 8564                                                                                           zinc finger DBF-type containing 2
## 8603                                                                                    pleckstrin homology domain containing M3
## 8611                                                                                                          crystallin gamma D
## 8613                                                                                                          crystallin gamma C
## 9027                                                                                      inositol polyphosphate-5-phosphatase D
## 9030                                                                                                 autophagy related 16 like 1
## 9032                                                                                             small Cajal body-specific RNA 5
## 9034                                                                                             small Cajal body-specific RNA 6
## 9036                                                                                                   S-antigen visual arrestin
## 9039                                                                                                 diacylglycerol kinase delta
## 9140                                                                                    twist family bHLH transcription factor 2
## 9227                                                                                            galactose-3-O-sulfotransferase 2
## 9231                                                                                                             neuraminidase 4
## 9234                                                                                                     programmed cell death 1
## 9402                                                           TAM41 mitochondrial translocator assembly and maintenance homolog
## 9512                                                                                                      phospholipase C like 2
## 9514                                                                                                               microRNA 3714
## 9881                                                                                                     zinc finger protein 445
## 9883                                                                                                     zinc finger protein 852
## 9887                                                                                    zinc finger with KRAB and SCAN domains 7
## 9891                                                                                                     zinc finger protein 660
## 9894                                                                                                     zinc finger protein 197
## 9896                                                                                                      ZNF197 antisense RNA 1
## 9898                                                                                                      zinc finger protein 35
## 9902                                                                                                     zinc finger protein 502
## 9904                                                                                                     zinc finger protein 501
## 9906                                                                                                                    KIAA1143
## 9908                                                                                                    kinesin family member 15
## 9911                                                                                                    transmembrane protein 42
## 9913                                                                                                                microRNA 564
## 9915                                                                                                          transglutaminase 4
## 10118                                                                                           cytochrome b561 family member D2
## 10350                                                       membrane associated guanylate kinase, WW and PDZ domain containing 1
## 10360                                                                                         solute carrier family 25 member 26
## 10424                                                                                              RING1 and YY1 binding protein
## 10466                                                                    family with sequence similarity 86 member D, pseudogene
## 10527                                                                                 long intergenic non-protein coding RNA 971
## 10582                                                                                 long intergenic non-protein coding RNA 879
## 10782                                                                                         chromosome 3 open reading frame 52
## 10785                                                                          germinal center associated signaling and motility
## 10788                                                                                          solute carrier family 9 member C1
## 10817                                                                                 spindle and centriole associated protein 1
## 11066                                                                                                     RuvB like AAA ATPase 1
## 11071                                                                 eukaryotic elongation factor, selenocysteine-tRNA specific
## 11219                                                                                                     centrosomal protein 63
## 11495                                                                                           arylacetamide deacetylase like 2
## 11525                                                                                                   ARHGEF26 antisense RNA 1
## 11527                                                                                  Rho guanine nucleotide exchange factor 26
## 11529                                                                                                       DEAH-box helicase 36
## 11619                                                                                          schwannomin interacting protein 1
## 11803                                                                                                              microRNA 4789
## 12160                                                                                          mucin 20, cell surface associated
## 12161                                                                                          mucin 20, cell surface associated
## 12162                                                                                          mucin 20, cell surface associated
## 12163                                                                                          mucin 20, cell surface associated
## 12164                                                                                          mucin 20, cell surface associated
## 12165                                                                                          mucin 20, cell surface associated
## 12166                                                                                          mucin 20, cell surface associated
## 12168                                                                                           mucin 4, cell surface associated
## 12169                                                                                           mucin 4, cell surface associated
## 12170                                                                                           mucin 4, cell surface associated
## 12171                                                                                           mucin 4, cell surface associated
## 12172                                                                                           mucin 4, cell surface associated
## 12173                                                                                           mucin 4, cell surface associated
## 12174                                                                                           mucin 4, cell surface associated
## 12241                                                                                          3-hydroxybutyrate dehydrogenase 1
## 12261                                                                                      ankyrin repeat domain 18D, pseudogene
## 12336                                                                                family with sequence similarity 53 member A
## 12488                                                                                                       H6 family homeobox 1
## 12665                                                                      potassium voltage-gated channel interacting protein 4
## 12942                                                                                  transient erythroblastopenia of childhood
## 13184                                                                                                    YTH domain containing 1
## 13187                                                                                          transmembrane serine protease 11E
## 13194                                                                            UDP glucuronosyltransferase family 2 member B15
## 13199                                                                            UDP glucuronosyltransferase family 2 member B10
## 13209                                                                             UDP glucuronosyltransferase family 2 member A3
## 13247                                                                                                                casein beta
## 13249                                                                                                                  statherin
## 13251                                                                                                                 histatin 3
## 13253                                                                                                                 histatin 1
## 13255                                                                                         casein alpha s2 like A, pseudogene
## 13511                                                                                         chromosome 4 open reading frame 36
## 13554                                                               HECT and RLD domain containing E3 ubiquitin protein ligase 3
## 13888                                                                                       centrosomal protein 170 pseudogene 1
## 14310                                                                                                dachsous cadherin-related 2
## 14350                                                                           acid sensing ion channel subunit family member 5
## 14352                                                                                                 tryptophan 2,3-dioxygenase
## 14354                                                                                                                cathepsin O
## 14728                                                                                long intergenic non-protein coding RNA 1060
## 14746                                                                                                         FSHD region gene 1
## 14747                                                                                                         FSHD region gene 1
## 14748                                                                                                         FSHD region gene 1
## 14756                                                                                                         FSHD region gene 2
## 14757                                                                                                         FSHD region gene 2
## 14758                                                                                                         FSHD region gene 2
## 14770                                                                                                          double homeobox 4
## 14792                                                                                          solute carrier family 9 member A3
## 14797                                                                                                     centrosomal protein 72
## 14814                                                                                   NKD inhibitor of WNT signaling pathway 2
## 14816                                                                                          solute carrier family 12 member 7
## 14824                                                                                                                CLPTM1 like
## 14828                                                                                           solute carrier family 6 member 3
## 14830                                                                                  lysophosphatidylcholine acyltransferase 1
## 15219                                                                  ADAM metallopeptidase with thrombospondin type 1 motif 12
## 15222                                                                                          relaxin family peptide receptor 3
## 15224                                                                                          solute carrier family 45 member 2
## 15668                                                                                        mitochondrial ribosomal protein S36
## 15670                                                                                                  cyclin dependent kinase 7
## 15672                                                                                          coiled-coil domain containing 125
## 15677                                                                               TATA-box binding protein associated factor 9
## 15679                                                                                    RAD17 checkpoint clamp loader component
## 15681                                                                                                 MARVEL domain containing 2
## 15687                                                                                                                   occludin
## 15691                                                                                                     GTF2H2 family member C
## 15692                                                                                                     GTF2H2 family member C
## 15693                                                                                                     GTF2H2 family member C
## 15701                                                                                                  small EDRK-rich factor 1B
## 15702                                                                                                  small EDRK-rich factor 1B
## 15704                                                                                    survival of motor neuron 2, centromeric
## 15705                                                                                    survival of motor neuron 2, centromeric
## 15725                                                                                                  small EDRK-rich factor 1A
## 15726                                                                                                  small EDRK-rich factor 1A
## 15727                                                                                                  small EDRK-rich factor 1A
## 15728                                                                                                  small EDRK-rich factor 1A
## 15730                                                                                      survival of motor neuron 1, telomeric
## 15731                                                                                      survival of motor neuron 1, telomeric
## 15732                                                                                      survival of motor neuron 1, telomeric
## 15733                                                                                      survival of motor neuron 1, telomeric
## 15735                                                                                    NLR family apoptosis inhibitory protein
## 15736                                                                                    NLR family apoptosis inhibitory protein
## 15739                                                                                 general transcription factor IIH subunit 2
## 15740                                                                                 general transcription factor IIH subunit 2
## 15751                                                                      pro-melanin concentrating hormone like 2 (pseudogene)
## 15752                                                                      pro-melanin concentrating hormone like 2 (pseudogene)
## 15756                                       B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB
## 15757                                       B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB
## 15761                                                                                   methylcrotonyl-CoA carboxylase subunit 2
## 15762                                                                                   methylcrotonyl-CoA carboxylase subunit 2
## 15887                                                                                                       phosphodiesterase 8B
## 16753                                                                                                                   matrin 3
## 16764                                                                          DnaJ heat shock protein family (Hsp40) member C18
## 16767                                                      endothelial cell surface expressed chemotaxis and apoptosis regulator
## 16949                                                                                               RNA binding motif protein 27
## 17394                                                                               family with sequence similarity 153 member B
## 17467                                                                                                PROP paired-like homeobox 1
## 17468                                                                                                PROP paired-like homeobox 1
## 17502                                                                   ADAM metallopeptidase with thrombospondin type 1 motif 2
## 17512                                                                                           RUN and FYVE domain containing 1
## 17516                                                                                 heterogeneous nuclear ribonucleoprotein H1
## 17521                                                                                                     chibby family member 3
## 17523                                                                                                                   calnexin
## 17526                                                                              mastermind like transcriptional coactivator 1
## 17528                                                                                                    leukotriene C4 synthase
## 17530                                                   alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase B
## 17532                                                                                                              microRNA 1229
## 17534                                                                                                             sequestosome 1
## 17539                                                                                               TBC1 domain family member 9B
## 17676                                                                                family with sequence similarity 50 member B
## 17782                                                                      glucosaminyl (N-acetyl) transferase 2 (I blood group)
## 17788                                                                                         chromosome 6 open reading frame 52
## 17790                                                                                                 PAK1 interacting protein 1
## 17792                                                                                                  transmembrane protein 14C
## 18155                                                                                                   glutathione peroxidase 6
## 18157                                                                                                   glutathione peroxidase 5
## 18163                                                                                 long intergenic non-protein coding RNA 533
## 18173                                                                                                       HLA complex group 14
## 18174                                                                                                       HLA complex group 14
## 18175                                                                                                       HLA complex group 14
## 18176                                                                                                       HLA complex group 14
## 18177                                                                                                       HLA complex group 14
## 18179                                                                                             tripartite motif containing 27
## 18180                                                                                             tripartite motif containing 27
## 18181                                                                                             tripartite motif containing 27
## 18182                                                                                             tripartite motif containing 27
## 18183                                                                                             tripartite motif containing 27
## 18184                                                                                             tripartite motif containing 27
## 18192                                                                                                    zinc finger protein 311
## 18193                                                                                                    zinc finger protein 311
## 18194                                                                                                    zinc finger protein 311
## 18195                                                                                                    zinc finger protein 311
## 18196                                                                                                    zinc finger protein 311
## 18197                                                                                                    zinc finger protein 311
## 18200                                                                           olfactory receptor family 2 subfamily W member 1
## 18201                                                                           olfactory receptor family 2 subfamily W member 1
## 18202                                                                           olfactory receptor family 2 subfamily W member 1
## 18203                                                                           olfactory receptor family 2 subfamily W member 1
## 18204                                                                           olfactory receptor family 2 subfamily W member 1
## 18205                                                                           olfactory receptor family 2 subfamily W member 1
## 18206                                                                           olfactory receptor family 2 subfamily W member 1
## 18210                                                                           olfactory receptor family 2 subfamily B member 3
## 18211                                                                           olfactory receptor family 2 subfamily B member 3
## 18212                                                                           olfactory receptor family 2 subfamily B member 3
## 18213                                                                           olfactory receptor family 2 subfamily B member 3
## 18214                                                                           olfactory receptor family 2 subfamily B member 3
## 18215                                                                           olfactory receptor family 2 subfamily B member 3
## 18216                                                                           olfactory receptor family 2 subfamily B member 3
## 18218                                                                           olfactory receptor family 2 subfamily J member 1
## 18219                                                                           olfactory receptor family 2 subfamily J member 1
## 18220                                                                           olfactory receptor family 2 subfamily J member 1
## 18221                                                                           olfactory receptor family 2 subfamily J member 1
## 18222                                                                           olfactory receptor family 2 subfamily J member 1
## 18223                                                                           olfactory receptor family 2 subfamily J member 1
## 18224                                                                           olfactory receptor family 2 subfamily J member 1
## 18226                                                                           olfactory receptor family 2 subfamily J member 3
## 18227                                                                           olfactory receptor family 2 subfamily J member 3
## 18228                                                                           olfactory receptor family 2 subfamily J member 3
## 18229                                                                           olfactory receptor family 2 subfamily J member 3
## 18230                                                                           olfactory receptor family 2 subfamily J member 3
## 18231                                                                           olfactory receptor family 2 subfamily J member 3
## 18232                                                                           olfactory receptor family 2 subfamily J member 3
## 18236                                                                           olfactory receptor family 2 subfamily J member 2
## 18237                                                                           olfactory receptor family 2 subfamily J member 2
## 18238                                                                           olfactory receptor family 2 subfamily J member 2
## 18239                                                                           olfactory receptor family 2 subfamily J member 2
## 18240                                                                           olfactory receptor family 2 subfamily J member 2
## 18241                                                                           olfactory receptor family 2 subfamily J member 2
## 18242                                                                           olfactory receptor family 2 subfamily J member 2
## 18251                                                                          olfactory receptor family 14 subfamily J member 1
## 18252                                                                          olfactory receptor family 14 subfamily J member 1
## 18253                                                                          olfactory receptor family 14 subfamily J member 1
## 18254                                                                          olfactory receptor family 14 subfamily J member 1
## 18255                                                                          olfactory receptor family 14 subfamily J member 1
## 18256                                                                          olfactory receptor family 14 subfamily J member 1
## 18259                                                                           olfactory receptor family 5 subfamily V member 1
## 18260                                                                           olfactory receptor family 5 subfamily V member 1
## 18261                                                                           olfactory receptor family 5 subfamily V member 1
## 18262                                                                           olfactory receptor family 5 subfamily V member 1
## 18263                                                                           olfactory receptor family 5 subfamily V member 1
## 18264                                                                           olfactory receptor family 5 subfamily V member 1
## 18265                                                                           olfactory receptor family 5 subfamily V member 1
## 18267                                                                          olfactory receptor family 12 subfamily D member 3
## 18268                                                                          olfactory receptor family 12 subfamily D member 3
## 18269                                                                          olfactory receptor family 12 subfamily D member 3
## 18270                                                                          olfactory receptor family 12 subfamily D member 3
## 18271                                                                          olfactory receptor family 12 subfamily D member 3
## 18272                                                                          olfactory receptor family 12 subfamily D member 3
## 18274                                                                          olfactory receptor family 12 subfamily D member 2
## 18275                                                                          olfactory receptor family 12 subfamily D member 2
## 18276                                                                          olfactory receptor family 12 subfamily D member 2
## 18277                                                                          olfactory receptor family 12 subfamily D member 2
## 18278                                                                          olfactory receptor family 12 subfamily D member 2
## 18280                                                        olfactory receptor family 12 subfamily D member 1 (gene/pseudogene)
## 18281                                                        olfactory receptor family 12 subfamily D member 1 (gene/pseudogene)
## 18282                                                        olfactory receptor family 12 subfamily D member 1 (gene/pseudogene)
## 18283                                                        olfactory receptor family 12 subfamily D member 1 (gene/pseudogene)
## 18284                                                        olfactory receptor family 12 subfamily D member 1 (gene/pseudogene)
## 18285                                                        olfactory receptor family 12 subfamily D member 1 (gene/pseudogene)
## 18287                                                                          olfactory receptor family 11 subfamily A member 1
## 18288                                                                          olfactory receptor family 11 subfamily A member 1
## 18289                                                                          olfactory receptor family 11 subfamily A member 1
## 18290                                                                          olfactory receptor family 11 subfamily A member 1
## 18291                                                                          olfactory receptor family 11 subfamily A member 1
## 18292                                                                          olfactory receptor family 11 subfamily A member 1
## 18293                                                                          olfactory receptor family 11 subfamily A member 1
## 18295                                                                          olfactory receptor family 10 subfamily C member 1
## 18296                                                                          olfactory receptor family 10 subfamily C member 1
## 18297                                                                          olfactory receptor family 10 subfamily C member 1
## 18298                                                                          olfactory receptor family 10 subfamily C member 1
## 18299                                                                          olfactory receptor family 10 subfamily C member 1
## 18300                                                                          olfactory receptor family 10 subfamily C member 1
## 18301                                                                          olfactory receptor family 10 subfamily C member 1
## 18303                                                                           olfactory receptor family 2 subfamily H member 1
## 18304                                                                           olfactory receptor family 2 subfamily H member 1
## 18305                                                                           olfactory receptor family 2 subfamily H member 1
## 18306                                                                           olfactory receptor family 2 subfamily H member 1
## 18307                                                                           olfactory receptor family 2 subfamily H member 1
## 18308                                                                           olfactory receptor family 2 subfamily H member 1
## 18309                                                                           olfactory receptor family 2 subfamily H member 1
## 18313                                                                       MAS1 proto-oncogene like, G protein-coupled receptor
## 18314                                                                       MAS1 proto-oncogene like, G protein-coupled receptor
## 18315                                                                       MAS1 proto-oncogene like, G protein-coupled receptor
## 18316                                                                       MAS1 proto-oncogene like, G protein-coupled receptor
## 18317                                                                       MAS1 proto-oncogene like, G protein-coupled receptor
## 18318                                                                       MAS1 proto-oncogene like, G protein-coupled receptor
## 18319                                                                       MAS1 proto-oncogene like, G protein-coupled receptor
## 18323                                                                                long intergenic non-protein coding RNA 1015
## 18324                                                                                long intergenic non-protein coding RNA 1015
## 18325                                                                                long intergenic non-protein coding RNA 1015
## 18326                                                                                long intergenic non-protein coding RNA 1015
## 18327                                                                                long intergenic non-protein coding RNA 1015
## 18328                                                                                long intergenic non-protein coding RNA 1015
## 18329                                                                                long intergenic non-protein coding RNA 1015
## 18333                                                                                                                ubiquitin D
## 18334                                                                                                                ubiquitin D
## 18335                                                                                                                ubiquitin D
## 18336                                                                                                                ubiquitin D
## 18337                                                                                                                ubiquitin D
## 18338                                                                                                                ubiquitin D
## 18340                                                                          gamma-aminobutyric acid type B receptor subunit 1
## 18341                                                                          gamma-aminobutyric acid type B receptor subunit 1
## 18342                                                                          gamma-aminobutyric acid type B receptor subunit 1
## 18343                                                                          gamma-aminobutyric acid type B receptor subunit 1
## 18344                                                                          gamma-aminobutyric acid type B receptor subunit 1
## 18345                                                                          gamma-aminobutyric acid type B receptor subunit 1
## 18349                                                                                           small nucleolar RNA, C/D box 32B
## 18350                                                                                           small nucleolar RNA, C/D box 32B
## 18351                                                                                           small nucleolar RNA, C/D box 32B
## 18352                                                                                           small nucleolar RNA, C/D box 32B
## 18353                                                                                           small nucleolar RNA, C/D box 32B
## 18354                                                                                           small nucleolar RNA, C/D box 32B
## 18357                                                                           olfactory receptor family 2 subfamily H member 2
## 18358                                                                           olfactory receptor family 2 subfamily H member 2
## 18359                                                                           olfactory receptor family 2 subfamily H member 2
## 18360                                                                           olfactory receptor family 2 subfamily H member 2
## 18361                                                                           olfactory receptor family 2 subfamily H member 2
## 18362                                                                           olfactory receptor family 2 subfamily H member 2
## 18365                                                                                        myelin oligodendrocyte glycoprotein
## 18366                                                                                        myelin oligodendrocyte glycoprotein
## 18367                                                                                        myelin oligodendrocyte glycoprotein
## 18368                                                                                        myelin oligodendrocyte glycoprotein
## 18369                                                                                        myelin oligodendrocyte glycoprotein
## 18370                                                                                        myelin oligodendrocyte glycoprotein
## 18371                                                                                        myelin oligodendrocyte glycoprotein
## 18373                                                                                                  ZFP57 zinc finger protein
## 18374                                                                                                  ZFP57 zinc finger protein
## 18375                                                                                                  ZFP57 zinc finger protein
## 18376                                                                                                  ZFP57 zinc finger protein
## 18377                                                                                                  ZFP57 zinc finger protein
## 18378                                                                                                  ZFP57 zinc finger protein
## 18379                                                                                                  ZFP57 zinc finger protein
## 18382                                                                               major histocompatibility complex, class I, F
## 18383                                                                               major histocompatibility complex, class I, F
## 18384                                                                               major histocompatibility complex, class I, F
## 18385                                                                               major histocompatibility complex, class I, F
## 18386                                                                               major histocompatibility complex, class I, F
## 18387                                                                               major histocompatibility complex, class I, F
## 18390                                                                                                      HLA-F antisense RNA 1
## 18391                                                                                                      HLA-F antisense RNA 1
## 18392                                                                                                      HLA-F antisense RNA 1
## 18393                                                                                                      HLA-F antisense RNA 1
## 18394                                                                                                      HLA-F antisense RNA 1
## 18402                                                                  major histocompatibility complex, class I, V (pseudogene)
## 18403                                                                  major histocompatibility complex, class I, V (pseudogene)
## 18404                                                                  major histocompatibility complex, class I, V (pseudogene)
## 18405                                                                  major histocompatibility complex, class I, V (pseudogene)
## 18406                                                                  major histocompatibility complex, class I, V (pseudogene)
## 18407                                                                  major histocompatibility complex, class I, V (pseudogene)
## 18408                                                                  major histocompatibility complex, class I, V (pseudogene)
## 18414                                                                               major histocompatibility complex, class I, G
## 18415                                                                               major histocompatibility complex, class I, G
## 18416                                                                               major histocompatibility complex, class I, G
## 18417                                                                               major histocompatibility complex, class I, G
## 18418                                                                               major histocompatibility complex, class I, G
## 18419                                                                               major histocompatibility complex, class I, G
## 18420                                                                               major histocompatibility complex, class I, G
## 18432                                                                               major histocompatibility complex, class I, A
## 18433                                                                               major histocompatibility complex, class I, A
## 18434                                                                               major histocompatibility complex, class I, A
## 18435                                                                               major histocompatibility complex, class I, A
## 18436                                                                               major histocompatibility complex, class I, A
## 18437                                                                               major histocompatibility complex, class I, A
## 18438                                                                               major histocompatibility complex, class I, A
## 18443                                                                                                        HLA complex group 9
## 18444                                                                                                        HLA complex group 9
## 18445                                                                                                        HLA complex group 9
## 18446                                                                                                        HLA complex group 9
## 18447                                                                                                        HLA complex group 9
## 18448                                                                                                        HLA complex group 9
## 18457                                                                      protein phosphatase 1 regulatory inhibitor subunit 11
## 18458                                                                      protein phosphatase 1 regulatory inhibitor subunit 11
## 18459                                                                      protein phosphatase 1 regulatory inhibitor subunit 11
## 18460                                                                      protein phosphatase 1 regulatory inhibitor subunit 11
## 18461                                                                      protein phosphatase 1 regulatory inhibitor subunit 11
## 18462                                                                      protein phosphatase 1 regulatory inhibitor subunit 11
## 18463                                                                      protein phosphatase 1 regulatory inhibitor subunit 11
## 18465                                                                                                     ring finger protein 39
## 18466                                                                                                     ring finger protein 39
## 18467                                                                                                     ring finger protein 39
## 18468                                                                                                     ring finger protein 39
## 18469                                                                                                     ring finger protein 39
## 18470                                                                                                     ring finger protein 39
## 18471                                                                                                     ring finger protein 39
## 18474                                                                                             tripartite motif containing 31
## 18475                                                                                             tripartite motif containing 31
## 18476                                                                                             tripartite motif containing 31
## 18477                                                                                             tripartite motif containing 31
## 18478                                                                                             tripartite motif containing 31
## 18479                                                                                             tripartite motif containing 31
## 18480                                                                                             tripartite motif containing 31
## 18482                                                                                                     TRIM31 antisense RNA 1
## 18483                                                                                                     TRIM31 antisense RNA 1
## 18484                                                                                                     TRIM31 antisense RNA 1
## 18485                                                                                                     TRIM31 antisense RNA 1
## 18486                                                                                                     TRIM31 antisense RNA 1
## 18487                                                                                                     TRIM31 antisense RNA 1
## 18488                                                                                                     TRIM31 antisense RNA 1
## 18490                                                                                             tripartite motif containing 40
## 18491                                                                                             tripartite motif containing 40
## 18492                                                                                             tripartite motif containing 40
## 18493                                                                                             tripartite motif containing 40
## 18494                                                                                             tripartite motif containing 40
## 18495                                                                                             tripartite motif containing 40
## 18496                                                                                             tripartite motif containing 40
## 18498                                                                                             tripartite motif containing 10
## 18499                                                                                             tripartite motif containing 10
## 18500                                                                                             tripartite motif containing 10
## 18501                                                                                             tripartite motif containing 10
## 18502                                                                                             tripartite motif containing 10
## 18503                                                                                             tripartite motif containing 10
## 18504                                                                                             tripartite motif containing 10
## 18506                                                                                             tripartite motif containing 15
## 18507                                                                                             tripartite motif containing 15
## 18508                                                                                             tripartite motif containing 15
## 18509                                                                                             tripartite motif containing 15
## 18510                                                                                             tripartite motif containing 15
## 18511                                                                                             tripartite motif containing 15
## 18512                                                                                             tripartite motif containing 15
## 18514                                                                                             tripartite motif containing 26
## 18515                                                                                             tripartite motif containing 26
## 18516                                                                                             tripartite motif containing 26
## 18517                                                                                             tripartite motif containing 26
## 18518                                                                                             tripartite motif containing 26
## 18519                                                                                             tripartite motif containing 26
## 18520                                                                                             tripartite motif containing 26
## 18523                                                                                                       HLA complex group 17
## 18524                                                                                                       HLA complex group 17
## 18525                                                                                                       HLA complex group 17
## 18526                                                                                                       HLA complex group 17
## 18527                                                                                                       HLA complex group 17
## 18528                                                                                                       HLA complex group 17
## 18531                                                                  major histocompatibility complex, class I, L (pseudogene)
## 18532                                                                  major histocompatibility complex, class I, L (pseudogene)
## 18533                                                                  major histocompatibility complex, class I, L (pseudogene)
## 18534                                                                  major histocompatibility complex, class I, L (pseudogene)
## 18535                                                                  major histocompatibility complex, class I, L (pseudogene)
## 18537                                                                                                       HLA complex group 18
## 18538                                                                                                       HLA complex group 18
## 18539                                                                                                       HLA complex group 18
## 18540                                                                                                       HLA complex group 18
## 18541                                                                                                       HLA complex group 18
## 18542                                                                                                       HLA complex group 18
## 18544                                                                                             tripartite motif containing 39
## 18545                                                                                             tripartite motif containing 39
## 18546                                                                                             tripartite motif containing 39
## 18547                                                                                             tripartite motif containing 39
## 18548                                                                                             tripartite motif containing 39
## 18549                                                                                             tripartite motif containing 39
## 18551                                                                                                   TRIM39-RPP21 readthrough
## 18552                                                                                                   TRIM39-RPP21 readthrough
## 18553                                                                                                   TRIM39-RPP21 readthrough
## 18554                                                                                                   TRIM39-RPP21 readthrough
## 18555                                                                                                   TRIM39-RPP21 readthrough
## 18556                                                                                                   TRIM39-RPP21 readthrough
## 18557                                                                                                   TRIM39-RPP21 readthrough
## 18559                                                                                             ribonuclease P/MRP subunit p21
## 18560                                                                                             ribonuclease P/MRP subunit p21
## 18561                                                                                             ribonuclease P/MRP subunit p21
## 18562                                                                                             ribonuclease P/MRP subunit p21
## 18563                                                                                             ribonuclease P/MRP subunit p21
## 18564                                                                                             ribonuclease P/MRP subunit p21
## 18573                                                                               major histocompatibility complex, class I, E
## 18574                                                                               major histocompatibility complex, class I, E
## 18575                                                                               major histocompatibility complex, class I, E
## 18576                                                                               major histocompatibility complex, class I, E
## 18577                                                                               major histocompatibility complex, class I, E
## 18578                                                                               major histocompatibility complex, class I, E
## 18581                                                                                           G protein nucleolar 1 (putative)
## 18582                                                                                           G protein nucleolar 1 (putative)
## 18583                                                                                           G protein nucleolar 1 (putative)
## 18584                                                                                           G protein nucleolar 1 (putative)
## 18585                                                                                           G protein nucleolar 1 (putative)
## 18586                                                                                           G protein nucleolar 1 (putative)
## 18587                                                                                           G protein nucleolar 1 (putative)
## 18589                                                                                                             proline rich 3
## 18590                                                                                                             proline rich 3
## 18591                                                                                                             proline rich 3
## 18592                                                                                                             proline rich 3
## 18593                                                                                                             proline rich 3
## 18594                                                                                                             proline rich 3
## 18596                                                                                  ATP binding cassette subfamily F member 1
## 18597                                                                                  ATP binding cassette subfamily F member 1
## 18598                                                                                  ATP binding cassette subfamily F member 1
## 18599                                                                                  ATP binding cassette subfamily F member 1
## 18600                                                                                  ATP binding cassette subfamily F member 1
## 18601                                                                                  ATP binding cassette subfamily F member 1
## 18604                                                                                protein phosphatase 1 regulatory subunit 10
## 18605                                                                                protein phosphatase 1 regulatory subunit 10
## 18606                                                                                protein phosphatase 1 regulatory subunit 10
## 18607                                                                                protein phosphatase 1 regulatory subunit 10
## 18608                                                                                protein phosphatase 1 regulatory subunit 10
## 18609                                                                                protein phosphatase 1 regulatory subunit 10
## 18612                                                                                       mitochondrial ribosomal protein S18B
## 18613                                                                                       mitochondrial ribosomal protein S18B
## 18614                                                                                       mitochondrial ribosomal protein S18B
## 18615                                                                                       mitochondrial ribosomal protein S18B
## 18616                                                                                       mitochondrial ribosomal protein S18B
## 18617                                                                                       mitochondrial ribosomal protein S18B
## 18619                                                                                          alpha tubulin acetyltransferase 1
## 18620                                                                                          alpha tubulin acetyltransferase 1
## 18621                                                                                          alpha tubulin acetyltransferase 1
## 18622                                                                                          alpha tubulin acetyltransferase 1
## 18623                                                                                          alpha tubulin acetyltransferase 1
## 18624                                                                                          alpha tubulin acetyltransferase 1
## 18627                                                                                        chromosome 6 open reading frame 136
## 18628                                                                                        chromosome 6 open reading frame 136
## 18629                                                                                        chromosome 6 open reading frame 136
## 18630                                                                                        chromosome 6 open reading frame 136
## 18631                                                                                        chromosome 6 open reading frame 136
## 18632                                                                                        chromosome 6 open reading frame 136
## 18635                                                                                                       DEAH-box helicase 16
## 18636                                                                                                       DEAH-box helicase 16
## 18637                                                                                                       DEAH-box helicase 16
## 18638                                                                                                       DEAH-box helicase 16
## 18639                                                                                                       DEAH-box helicase 16
## 18640                                                                                                       DEAH-box helicase 16
## 18641                                                                                                       DEAH-box helicase 16
## 18643                                                                                protein phosphatase 1 regulatory subunit 18
## 18644                                                                                protein phosphatase 1 regulatory subunit 18
## 18645                                                                                protein phosphatase 1 regulatory subunit 18
## 18646                                                                                protein phosphatase 1 regulatory subunit 18
## 18647                                                                                protein phosphatase 1 regulatory subunit 18
## 18648                                                                                protein phosphatase 1 regulatory subunit 18
## 18649                                                                                protein phosphatase 1 regulatory subunit 18
## 18651                                                                                                                      nurim
## 18652                                                                                                                      nurim
## 18653                                                                                                                      nurim
## 18654                                                                                                                      nurim
## 18655                                                                                                                      nurim
## 18656                                                                                                                      nurim
## 18659                                                                                        mediator of DNA damage checkpoint 1
## 18660                                                                                        mediator of DNA damage checkpoint 1
## 18661                                                                                        mediator of DNA damage checkpoint 1
## 18662                                                                                        mediator of DNA damage checkpoint 1
## 18663                                                                                        mediator of DNA damage checkpoint 1
## 18664                                                                                        mediator of DNA damage checkpoint 1
## 18665                                                                                        mediator of DNA damage checkpoint 1
## 18667                                                                                                       MDC1 antisense RNA 1
## 18668                                                                                                       MDC1 antisense RNA 1
## 18669                                                                                                       MDC1 antisense RNA 1
## 18670                                                                                                       MDC1 antisense RNA 1
## 18671                                                                                                       MDC1 antisense RNA 1
## 18672                                                                                                       MDC1 antisense RNA 1
## 18673                                                                                                       MDC1 antisense RNA 1
## 18675                                                                                                       tubulin beta class I
## 18676                                                                                                       tubulin beta class I
## 18677                                                                                                       tubulin beta class I
## 18678                                                                                                       tubulin beta class I
## 18679                                                                                                       tubulin beta class I
## 18680                                                                                                       tubulin beta class I
## 18681                                                                                                       tubulin beta class I
## 18684                                                                                                                flotillin 1
## 18685                                                                                                                flotillin 1
## 18686                                                                                                                flotillin 1
## 18687                                                                                                                flotillin 1
## 18688                                                                                                                flotillin 1
## 18689                                                                                                                flotillin 1
## 18690                                                                                                                flotillin 1
## 18693                                                                                                 immediate early response 3
## 18694                                                                                                 immediate early response 3
## 18695                                                                                                 immediate early response 3
## 18696                                                                                                 immediate early response 3
## 18697                                                                                                 immediate early response 3
## 18700                                                                                                       HLA complex group 20
## 18701                                                                                                       HLA complex group 20
## 18702                                                                                                       HLA complex group 20
## 18703                                                                                                       HLA complex group 20
## 18704                                                                                                       HLA complex group 20
## 18706                                                                                 long intergenic non-protein coding RNA 243
## 18707                                                                                 long intergenic non-protein coding RNA 243
## 18708                                                                                 long intergenic non-protein coding RNA 243
## 18709                                                                                 long intergenic non-protein coding RNA 243
## 18710                                                                                 long intergenic non-protein coding RNA 243
## 18715                                                                                discoidin domain receptor tyrosine kinase 1
## 18716                                                                                discoidin domain receptor tyrosine kinase 1
## 18717                                                                                discoidin domain receptor tyrosine kinase 1
## 18718                                                                                discoidin domain receptor tyrosine kinase 1
## 18719                                                                                discoidin domain receptor tyrosine kinase 1
## 18720                                                                                discoidin domain receptor tyrosine kinase 1
## 18724                                                                                 general transcription factor IIH subunit 4
## 18725                                                                                 general transcription factor IIH subunit 4
## 18726                                                                                 general transcription factor IIH subunit 4
## 18727                                                                                 general transcription factor IIH subunit 4
## 18728                                                                                 general transcription factor IIH subunit 4
## 18730                                                                                     valyl-tRNA synthetase 2, mitochondrial
## 18731                                                                                     valyl-tRNA synthetase 2, mitochondrial
## 18732                                                                                     valyl-tRNA synthetase 2, mitochondrial
## 18733                                                                                     valyl-tRNA synthetase 2, mitochondrial
## 18734                                                                                     valyl-tRNA synthetase 2, mitochondrial
## 18736                                                                                                    surfactant associated 2
## 18737                                                                                                    surfactant associated 2
## 18738                                                                                                    surfactant associated 2
## 18739                                                                                                    surfactant associated 2
## 18740                                                                                                    surfactant associated 2
## 18744                                                                                          mucin 21, cell surface associated
## 18745                                                                                          mucin 21, cell surface associated
## 18746                                                                                          mucin 21, cell surface associated
## 18747                                                                                          mucin 21, cell surface associated
## 18748                                                                                          mucin 21, cell surface associated
## 18749                                                                                          mucin 21, cell surface associated
## 18752                                                                                     HLA complex group 22 (gene/pseudogene)
## 18753                                                                                     HLA complex group 22 (gene/pseudogene)
## 18754                                                                                     HLA complex group 22 (gene/pseudogene)
## 18755                                                                                     HLA complex group 22 (gene/pseudogene)
## 18756                                                                                     HLA complex group 22 (gene/pseudogene)
## 18757                                                                                     HLA complex group 22 (gene/pseudogene)
## 18758                                                                                     HLA complex group 22 (gene/pseudogene)
## 18761                                                                                         chromosome 6 open reading frame 15
## 18762                                                                                         chromosome 6 open reading frame 15
## 18763                                                                                         chromosome 6 open reading frame 15
## 18764                                                                                         chromosome 6 open reading frame 15
## 18765                                                                                         chromosome 6 open reading frame 15
## 18767                                                                                     psoriasis susceptibility 1 candidate 1
## 18768                                                                                     psoriasis susceptibility 1 candidate 1
## 18769                                                                                     psoriasis susceptibility 1 candidate 1
## 18770                                                                                     psoriasis susceptibility 1 candidate 1
## 18771                                                                                     psoriasis susceptibility 1 candidate 1
## 18773                                                                                                             corneodesmosin
## 18774                                                                                                             corneodesmosin
## 18775                                                                                                             corneodesmosin
## 18776                                                                                                             corneodesmosin
## 18777                                                                                                             corneodesmosin
## 18779                                                                                     psoriasis susceptibility 1 candidate 2
## 18780                                                                                     psoriasis susceptibility 1 candidate 2
## 18781                                                                                     psoriasis susceptibility 1 candidate 2
## 18782                                                                                     psoriasis susceptibility 1 candidate 2
## 18783                                                                                     psoriasis susceptibility 1 candidate 2
## 18786                                                                                    coiled-coil alpha-helical rod protein 1
## 18787                                                                                    coiled-coil alpha-helical rod protein 1
## 18788                                                                                    coiled-coil alpha-helical rod protein 1
## 18789                                                                                    coiled-coil alpha-helical rod protein 1
## 18790                                                                                    coiled-coil alpha-helical rod protein 1
## 18792                                                                                                    transcription factor 19
## 18793                                                                                                    transcription factor 19
## 18794                                                                                                    transcription factor 19
## 18795                                                                                                    transcription factor 19
## 18796                                                                                                    transcription factor 19
## 18797                                                                                                    transcription factor 19
## 18799                                                                                                     POU class 5 homeobox 1
## 18800                                                                                                     POU class 5 homeobox 1
## 18801                                                                                                     POU class 5 homeobox 1
## 18802                                                                                                     POU class 5 homeobox 1
## 18803                                                                                                     POU class 5 homeobox 1
## 18804                                                                                                     POU class 5 homeobox 1
## 18808                                                                                                       HLA complex group 27
## 18809                                                                                                       HLA complex group 27
## 18810                                                                                                       HLA complex group 27
## 18811                                                                                                       HLA complex group 27
## 18812                                                                                                       HLA complex group 27
## 18813                                                                                                       HLA complex group 27
## 18818                                                                               major histocompatibility complex, class I, C
## 18819                                                                               major histocompatibility complex, class I, C
## 18820                                                                               major histocompatibility complex, class I, C
## 18821                                                                               major histocompatibility complex, class I, C
## 18822                                                                               major histocompatibility complex, class I, C
## 18823                                                                               major histocompatibility complex, class I, C
## 18830                                                                               major histocompatibility complex, class I, B
## 18831                                                                               major histocompatibility complex, class I, B
## 18832                                                                               major histocompatibility complex, class I, B
## 18833                                                                               major histocompatibility complex, class I, B
## 18834                                                                               major histocompatibility complex, class I, B
## 18844                                                                                                             HLA complex P5
## 18845                                                                                                             HLA complex P5
## 18846                                                                                                             HLA complex P5
## 18848                                                                                 MHC class I polypeptide-related sequence A
## 18849                                                                                 MHC class I polypeptide-related sequence A
## 18850                                                                                 MHC class I polypeptide-related sequence A
## 18851                                                                                 MHC class I polypeptide-related sequence A
## 18855                                                                                 MHC class I polypeptide-related sequence B
## 18856                                                                                 MHC class I polypeptide-related sequence B
## 18857                                                                                 MHC class I polypeptide-related sequence B
## 18858                                                                                 MHC class I polypeptide-related sequence B
## 18859                                                                                 MHC class I polypeptide-related sequence B
## 18860                                                                                 MHC class I polypeptide-related sequence B
## 18861                                                                                 MHC class I polypeptide-related sequence B
## 18866                                                                                         mitochondrial coiled-coil domain 1
## 18867                                                                                         mitochondrial coiled-coil domain 1
## 18868                                                                                         mitochondrial coiled-coil domain 1
## 18869                                                                                         mitochondrial coiled-coil domain 1
## 18870                                                                                         mitochondrial coiled-coil domain 1
## 18871                                                                                         mitochondrial coiled-coil domain 1
## 18872                                                                                         mitochondrial coiled-coil domain 1
## 18875                                                                                                      DExD-box helicase 39B
## 18876                                                                                                      DExD-box helicase 39B
## 18877                                                                                                      DExD-box helicase 39B
## 18878                                                                                                      DExD-box helicase 39B
## 18879                                                                                                      DExD-box helicase 39B
## 18880                                                                                                      DExD-box helicase 39B
## 18881                                                                                                      DExD-box helicase 39B
## 18883                                                                                           small nucleolar RNA, C/D box 117
## 18884                                                                                           small nucleolar RNA, C/D box 117
## 18885                                                                                           small nucleolar RNA, C/D box 117
## 18886                                                                                           small nucleolar RNA, C/D box 117
## 18887                                                                                           small nucleolar RNA, C/D box 117
## 18888                                                                                           small nucleolar RNA, C/D box 117
## 18889                                                                                           small nucleolar RNA, C/D box 117
## 18891                                                                                            small nucleolar RNA, C/D box 84
## 18892                                                                                            small nucleolar RNA, C/D box 84
## 18893                                                                                            small nucleolar RNA, C/D box 84
## 18894                                                                                            small nucleolar RNA, C/D box 84
## 18895                                                                                            small nucleolar RNA, C/D box 84
## 18896                                                                                            small nucleolar RNA, C/D box 84
## 18898                                                                                                     DDX39B antisense RNA 1
## 18899                                                                                                     DDX39B antisense RNA 1
## 18900                                                                                                     DDX39B antisense RNA 1
## 18901                                                                                                     DDX39B antisense RNA 1
## 18902                                                                                                     DDX39B antisense RNA 1
## 18903                                                                                                     DDX39B antisense RNA 1
## 18905                                                                                       ATPase H+ transporting V1 subunit G2
## 18906                                                                                       ATPase H+ transporting V1 subunit G2
## 18907                                                                                       ATPase H+ transporting V1 subunit G2
## 18908                                                                                       ATPase H+ transporting V1 subunit G2
## 18909                                                                                       ATPase H+ transporting V1 subunit G2
## 18910                                                                                       ATPase H+ transporting V1 subunit G2
## 18912                                                                                                      NFKB inhibitor like 1
## 18913                                                                                                      NFKB inhibitor like 1
## 18914                                                                                                      NFKB inhibitor like 1
## 18915                                                                                                      NFKB inhibitor like 1
## 18916                                                                                                      NFKB inhibitor like 1
## 18917                                                                                                      NFKB inhibitor like 1
## 18919                                                                                                          lymphotoxin alpha
## 18920                                                                                                          lymphotoxin alpha
## 18921                                                                                                          lymphotoxin alpha
## 18922                                                                                                          lymphotoxin alpha
## 18923                                                                                                          lymphotoxin alpha
## 18924                                                                                                          lymphotoxin alpha
## 18926                                                                                                      tumor necrosis factor
## 18927                                                                                                      tumor necrosis factor
## 18928                                                                                                      tumor necrosis factor
## 18929                                                                                                      tumor necrosis factor
## 18930                                                                                                      tumor necrosis factor
## 18931                                                                                                      tumor necrosis factor
## 18932                                                                                                      tumor necrosis factor
## 18934                                                                                                           lymphotoxin beta
## 18935                                                                                                           lymphotoxin beta
## 18936                                                                                                           lymphotoxin beta
## 18937                                                                                                           lymphotoxin beta
## 18938                                                                                                           lymphotoxin beta
## 18939                                                                                                           lymphotoxin beta
## 18940                                                                                                           lymphotoxin beta
## 18942                                                                                            leukocyte specific transcript 1
## 18943                                                                                            leukocyte specific transcript 1
## 18944                                                                                            leukocyte specific transcript 1
## 18945                                                                                            leukocyte specific transcript 1
## 18946                                                                                            leukocyte specific transcript 1
## 18947                                                                                            leukocyte specific transcript 1
## 18948                                                                                            leukocyte specific transcript 1
## 18950                                                                                 natural cytotoxicity triggering receptor 3
## 18951                                                                                 natural cytotoxicity triggering receptor 3
## 18952                                                                                 natural cytotoxicity triggering receptor 3
## 18953                                                                                 natural cytotoxicity triggering receptor 3
## 18954                                                                                 natural cytotoxicity triggering receptor 3
## 18955                                                                                 natural cytotoxicity triggering receptor 3
## 18956                                                                                 natural cytotoxicity triggering receptor 3
## 18959                                                                                            allograft inflammatory factor 1
## 18960                                                                                            allograft inflammatory factor 1
## 18961                                                                                            allograft inflammatory factor 1
## 18962                                                                                            allograft inflammatory factor 1
## 18963                                                                                            allograft inflammatory factor 1
## 18965                                                                                                proline rich coiled-coil 2A
## 18966                                                                                                proline rich coiled-coil 2A
## 18967                                                                                                proline rich coiled-coil 2A
## 18968                                                                                                proline rich coiled-coil 2A
## 18969                                                                                                proline rich coiled-coil 2A
## 18970                                                                                                proline rich coiled-coil 2A
## 18972                                                                                          small nucleolar RNA, H/ACA box 38
## 18973                                                                                          small nucleolar RNA, H/ACA box 38
## 18974                                                                                          small nucleolar RNA, H/ACA box 38
## 18975                                                                                          small nucleolar RNA, H/ACA box 38
## 18976                                                                                          small nucleolar RNA, H/ACA box 38
## 18977                                                                                          small nucleolar RNA, H/ACA box 38
## 18979                                                                                                          BAG cochaperone 6
## 18980                                                                                                          BAG cochaperone 6
## 18981                                                                                                          BAG cochaperone 6
## 18982                                                                                                          BAG cochaperone 6
## 18983                                                                                                          BAG cochaperone 6
## 18984                                                                                                          BAG cochaperone 6
## 18986                                                                                                           apolipoprotein M
## 18987                                                                                                           apolipoprotein M
## 18988                                                                                                           apolipoprotein M
## 18989                                                                                                           apolipoprotein M
## 18990                                                                                                           apolipoprotein M
## 18991                                                                                                           apolipoprotein M
## 18993                                                                                         chromosome 6 open reading frame 47
## 18994                                                                                         chromosome 6 open reading frame 47
## 18995                                                                                         chromosome 6 open reading frame 47
## 18996                                                                                         chromosome 6 open reading frame 47
## 18997                                                                                         chromosome 6 open reading frame 47
## 18998                                                                                         chromosome 6 open reading frame 47
## 19001                                                                                       G-patch domain and ankyrin repeats 1
## 19002                                                                                       G-patch domain and ankyrin repeats 1
## 19003                                                                                       G-patch domain and ankyrin repeats 1
## 19004                                                                                       G-patch domain and ankyrin repeats 1
## 19005                                                                                       G-patch domain and ankyrin repeats 1
## 19006                                                                                       G-patch domain and ankyrin repeats 1
## 19008                                                                                                       casein kinase 2 beta
## 19009                                                                                                       casein kinase 2 beta
## 19010                                                                                                       casein kinase 2 beta
## 19011                                                                                                       casein kinase 2 beta
## 19012                                                                                                       casein kinase 2 beta
## 19013                                                                                                       casein kinase 2 beta
## 19016                                                                                     lymphocyte antigen 6 family member G5B
## 19017                                                                                     lymphocyte antigen 6 family member G5B
## 19018                                                                                     lymphocyte antigen 6 family member G5B
## 19019                                                                                     lymphocyte antigen 6 family member G5B
## 19020                                                                                     lymphocyte antigen 6 family member G5B
## 19021                                                                                     lymphocyte antigen 6 family member G5B
## 19023                                                                                     lymphocyte antigen 6 family member G5C
## 19024                                                                                     lymphocyte antigen 6 family member G5C
## 19025                                                                                     lymphocyte antigen 6 family member G5C
## 19026                                                                                     lymphocyte antigen 6 family member G5C
## 19027                                                                                     lymphocyte antigen 6 family member G5C
## 19028                                                                                     lymphocyte antigen 6 family member G5C
## 19030                                                                           abhydrolase domain containing 16A, phospholipase
## 19031                                                                           abhydrolase domain containing 16A, phospholipase
## 19032                                                                           abhydrolase domain containing 16A, phospholipase
## 19033                                                                           abhydrolase domain containing 16A, phospholipase
## 19034                                                                           abhydrolase domain containing 16A, phospholipase
## 19035                                                                           abhydrolase domain containing 16A, phospholipase
## 19039                                                                                     lymphocyte antigen 6 family member G6F
## 19040                                                                                     lymphocyte antigen 6 family member G6F
## 19041                                                                                     lymphocyte antigen 6 family member G6F
## 19042                                                                                     lymphocyte antigen 6 family member G6F
## 19043                                                                                     lymphocyte antigen 6 family member G6F
## 19044                                                                                     lymphocyte antigen 6 family member G6F
## 19048                                                                                     lymphocyte antigen 6 family member G6D
## 19049                                                                                     lymphocyte antigen 6 family member G6D
## 19050                                                                                     lymphocyte antigen 6 family member G6D
## 19051                                                                                     lymphocyte antigen 6 family member G6D
## 19052                                                                                     lymphocyte antigen 6 family member G6D
## 19053                                                                                     lymphocyte antigen 6 family member G6D
## 19056                                                                                     lymphocyte antigen 6 family member G6C
## 19057                                                                                     lymphocyte antigen 6 family member G6C
## 19058                                                                                     lymphocyte antigen 6 family member G6C
## 19059                                                                                     lymphocyte antigen 6 family member G6C
## 19060                                                                                     lymphocyte antigen 6 family member G6C
## 19061                                                                                     lymphocyte antigen 6 family member G6C
## 19063                                                                                  dimethylarginine dimethylaminohydrolase 2
## 19064                                                                                  dimethylarginine dimethylaminohydrolase 2
## 19065                                                                                  dimethylarginine dimethylaminohydrolase 2
## 19066                                                                                  dimethylarginine dimethylaminohydrolase 2
## 19067                                                                                  dimethylarginine dimethylaminohydrolase 2
## 19068                                                                                  dimethylarginine dimethylaminohydrolase 2
## 19070                                                                                           chloride intracellular channel 1
## 19071                                                                                           chloride intracellular channel 1
## 19072                                                                                           chloride intracellular channel 1
## 19073                                                                                           chloride intracellular channel 1
## 19074                                                                                           chloride intracellular channel 1
## 19075                                                                                           chloride intracellular channel 1
## 19077                                                                                                             mutS homolog 5
## 19078                                                                                                             mutS homolog 5
## 19079                                                                                                             mutS homolog 5
## 19080                                                                                                             mutS homolog 5
## 19081                                                                                                             mutS homolog 5
## 19082                                                                                                             mutS homolog 5
## 19083                                                                                                             mutS homolog 5
## 19087                                                                                         suppressor APC domain containing 1
## 19088                                                                                         suppressor APC domain containing 1
## 19089                                                                                         suppressor APC domain containing 1
## 19090                                                                                         suppressor APC domain containing 1
## 19091                                                                                         suppressor APC domain containing 1
## 19094                                                                                von Willebrand factor A domain containing 7
## 19095                                                                                von Willebrand factor A domain containing 7
## 19096                                                                                von Willebrand factor A domain containing 7
## 19097                                                                                von Willebrand factor A domain containing 7
## 19098                                                                                von Willebrand factor A domain containing 7
## 19101                                                         LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated
## 19102                                                         LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated
## 19103                                                         LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated
## 19104                                                         LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated
## 19105                                                         LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated
## 19107                                                                          heat shock protein family A (Hsp70) member 1 like
## 19108                                                                          heat shock protein family A (Hsp70) member 1 like
## 19109                                                                          heat shock protein family A (Hsp70) member 1 like
## 19110                                                                          heat shock protein family A (Hsp70) member 1 like
## 19112                                                                              heat shock protein family A (Hsp70) member 1A
## 19113                                                                              heat shock protein family A (Hsp70) member 1A
## 19114                                                                              heat shock protein family A (Hsp70) member 1A
## 19115                                                                              heat shock protein family A (Hsp70) member 1A
## 19117                                                                              heat shock protein family A (Hsp70) member 1B
## 19118                                                                              heat shock protein family A (Hsp70) member 1B
## 19119                                                                              heat shock protein family A (Hsp70) member 1B
## 19120                                                                              heat shock protein family A (Hsp70) member 1B
## 19123                                                                                            small nucleolar RNA, C/D box 48
## 19124                                                                                            small nucleolar RNA, C/D box 48
## 19125                                                                                            small nucleolar RNA, C/D box 48
## 19126                                                                                            small nucleolar RNA, C/D box 48
## 19128                                                                                            small nucleolar RNA, C/D box 52
## 19129                                                                                            small nucleolar RNA, C/D box 52
## 19130                                                                                            small nucleolar RNA, C/D box 52
## 19131                                                                                            small nucleolar RNA, C/D box 52
## 19133                                                                                                            neuraminidase 1
## 19134                                                                                                            neuraminidase 1
## 19135                                                                                                            neuraminidase 1
## 19136                                                                                                            neuraminidase 1
## 19137                                                                                                            neuraminidase 1
## 19138                                                                                                            neuraminidase 1
## 19139                                                                                                            neuraminidase 1
## 19141                                                                                          solute carrier family 44 member 4
## 19142                                                                                          solute carrier family 44 member 4
## 19143                                                                                          solute carrier family 44 member 4
## 19144                                                                                          solute carrier family 44 member 4
## 19145                                                                                          solute carrier family 44 member 4
## 19146                                                                                          solute carrier family 44 member 4
## 19147                                                                                          solute carrier family 44 member 4
## 19149                                                                             euchromatic histone lysine methyltransferase 2
## 19150                                                                             euchromatic histone lysine methyltransferase 2
## 19151                                                                             euchromatic histone lysine methyltransferase 2
## 19152                                                                             euchromatic histone lysine methyltransferase 2
## 19153                                                                             euchromatic histone lysine methyltransferase 2
## 19154                                                                             euchromatic histone lysine methyltransferase 2
## 19157                                                                                                              complement C2
## 19158                                                                                                              complement C2
## 19159                                                                                                              complement C2
## 19160                                                                                                              complement C2
## 19161                                                                                                              complement C2
## 19162                                                                                                              complement C2
## 19164                                                                                   zinc finger and BTB domain containing 12
## 19165                                                                                   zinc finger and BTB domain containing 12
## 19166                                                                                   zinc finger and BTB domain containing 12
## 19167                                                                                   zinc finger and BTB domain containing 12
## 19169                                                                                                        complement factor B
## 19170                                                                                                        complement factor B
## 19171                                                                                                        complement factor B
## 19172                                                                                                        complement factor B
## 19173                                                                                                        complement factor B
## 19174                                                                                                        complement factor B
## 19176                                                                                negative elongation factor complex member E
## 19177                                                                                negative elongation factor complex member E
## 19178                                                                                negative elongation factor complex member E
## 19179                                                                                negative elongation factor complex member E
## 19180                                                                                negative elongation factor complex member E
## 19183                                                                                                     Ski2 like RNA helicase
## 19184                                                                                                     Ski2 like RNA helicase
## 19185                                                                                                     Ski2 like RNA helicase
## 19186                                                                                                     Ski2 like RNA helicase
## 19187                                                                                                     Ski2 like RNA helicase
## 19189                                                                                                  decapping exoribonuclease
## 19190                                                                                                  decapping exoribonuclease
## 19191                                                                                                  decapping exoribonuclease
## 19192                                                                                                  decapping exoribonuclease
## 19193                                                                                                  decapping exoribonuclease
## 19195                                                                                                 serine/threonine kinase 19
## 19196                                                                                                 serine/threonine kinase 19
## 19197                                                                                                 serine/threonine kinase 19
## 19198                                                                                                 serine/threonine kinase 19
## 19199                                                                                                 serine/threonine kinase 19
## 19201                                                                                       complement C4A (Rodgers blood group)
## 19202                                                                                       complement C4A (Rodgers blood group)
## 19203                                                                                       complement C4A (Rodgers blood group)
## 19210                                                                                         complement C4B (Chido blood group)
## 19211                                                                                         complement C4B (Chido blood group)
## 19212                                                                                         complement C4B (Chido blood group)
## 19213                                                                                         complement C4B (Chido blood group)
## 19216                                                                             cytochrome P450 family 21 subfamily A member 2
## 19217                                                                             cytochrome P450 family 21 subfamily A member 2
## 19218                                                                             cytochrome P450 family 21 subfamily A member 2
## 19219                                                                             cytochrome P450 family 21 subfamily A member 2
## 19220                                                                             cytochrome P450 family 21 subfamily A member 2
## 19222                                                                                                                tenascin XB
## 19223                                                                                                                tenascin XB
## 19224                                                                                                                tenascin XB
## 19225                                                                                                                tenascin XB
## 19226                                                                                                                tenascin XB
## 19227                                                                                                                tenascin XB
## 19228                                                                                                                tenascin XB
## 19231                                                                                     activating transcription factor 6 beta
## 19232                                                                                     activating transcription factor 6 beta
## 19233                                                                                     activating transcription factor 6 beta
## 19235                                                                                                 FKBP prolyl isomerase like
## 19236                                                                                                 FKBP prolyl isomerase like
## 19237                                                                                                 FKBP prolyl isomerase like
## 19239                                                                                       proline rich transmembrane protein 1
## 19240                                                                                       proline rich transmembrane protein 1
## 19241                                                                                       proline rich transmembrane protein 1
## 19242                                                                                       proline rich transmembrane protein 1
## 19243                                                                                       proline rich transmembrane protein 1
## 19244                                                                                       proline rich transmembrane protein 1
## 19245                                                                                       proline rich transmembrane protein 1
## 19247                                                                                           palmitoyl-protein thioesterase 2
## 19248                                                                                           palmitoyl-protein thioesterase 2
## 19249                                                                                           palmitoyl-protein thioesterase 2
## 19250                                                                                           palmitoyl-protein thioesterase 2
## 19251                                                                                           palmitoyl-protein thioesterase 2
## 19252                                                                                           palmitoyl-protein thioesterase 2
## 19253                                                                                           palmitoyl-protein thioesterase 2
## 19256                                                                                                 EGF like domain multiple 8
## 19257                                                                                                 EGF like domain multiple 8
## 19258                                                                                                 EGF like domain multiple 8
## 19259                                                                                                 EGF like domain multiple 8
## 19260                                                                                                 EGF like domain multiple 8
## 19261                                                                                                 EGF like domain multiple 8
## 19263                                                                             1-acylglycerol-3-phosphate O-acyltransferase 1
## 19264                                                                             1-acylglycerol-3-phosphate O-acyltransferase 1
## 19265                                                                             1-acylglycerol-3-phosphate O-acyltransferase 1
## 19266                                                                             1-acylglycerol-3-phosphate O-acyltransferase 1
## 19267                                                                             1-acylglycerol-3-phosphate O-acyltransferase 1
## 19268                                                                             1-acylglycerol-3-phosphate O-acyltransferase 1
## 19270                                                                                                      ring finger protein 5
## 19271                                                                                                      ring finger protein 5
## 19272                                                                                                      ring finger protein 5
## 19273                                                                                                      ring finger protein 5
## 19274                                                                                                      ring finger protein 5
## 19275                                                                                                      ring finger protein 5
## 19277                                                                       advanced glycosylation end-product specific receptor
## 19278                                                                       advanced glycosylation end-product specific receptor
## 19279                                                                       advanced glycosylation end-product specific receptor
## 19280                                                                       advanced glycosylation end-product specific receptor
## 19281                                                                       advanced glycosylation end-product specific receptor
## 19282                                                                       advanced glycosylation end-product specific receptor
## 19284                                                                                                             PBX homeobox 2
## 19285                                                                                                             PBX homeobox 2
## 19286                                                                                                             PBX homeobox 2
## 19287                                                                                                             PBX homeobox 2
## 19288                                                                                                             PBX homeobox 2
## 19289                                                                                                             PBX homeobox 2
## 19292                                                                                            G protein signaling modulator 3
## 19293                                                                                            G protein signaling modulator 3
## 19294                                                                                            G protein signaling modulator 3
## 19295                                                                                            G protein signaling modulator 3
## 19296                                                                                            G protein signaling modulator 3
## 19297                                                                                            G protein signaling modulator 3
## 19299                                                                                                           notch receptor 4
## 19300                                                                                                           notch receptor 4
## 19301                                                                                                           notch receptor 4
## 19302                                                                                                           notch receptor 4
## 19303                                                                                                           notch receptor 4
## 19304                                                                                                           notch receptor 4
## 19310                                                                                                       HLA complex group 23
## 19311                                                                                                       HLA complex group 23
## 19312                                                                                                       HLA complex group 23
## 19313                                                                                                       HLA complex group 23
## 19314                                                                                                       HLA complex group 23
## 19315                                                                                                       HLA complex group 23
## 19316                                                                                                       HLA complex group 23
## 19318                                                                                                        butyrophilin like 2
## 19319                                                                                                        butyrophilin like 2
## 19320                                                                                                        butyrophilin like 2
## 19321                                                                                                        butyrophilin like 2
## 19322                                                                                                        butyrophilin like 2
## 19323                                                                                                        butyrophilin like 2
## 19324                                                                                                        butyrophilin like 2
## 19325                                                                                                        butyrophilin like 2
## 19327                                                                       major histocompatibility complex, class II, DR alpha
## 19328                                                                       major histocompatibility complex, class II, DR alpha
## 19329                                                                       major histocompatibility complex, class II, DR alpha
## 19330                                                                       major histocompatibility complex, class II, DR alpha
## 19331                                                                       major histocompatibility complex, class II, DR alpha
## 19332                                                                       major histocompatibility complex, class II, DR alpha
## 19333                                                                       major histocompatibility complex, class II, DR alpha
## 19339                                                                      major histocompatibility complex, class II, DR beta 1
## 19340                                                                      major histocompatibility complex, class II, DR beta 1
## 19341                                                                      major histocompatibility complex, class II, DR beta 1
## 19342                                                                      major histocompatibility complex, class II, DR beta 1
## 19343                                                                      major histocompatibility complex, class II, DR beta 1
## 19345                                                                     major histocompatibility complex, class II, DQ alpha 1
## 19346                                                                     major histocompatibility complex, class II, DQ alpha 1
## 19347                                                                     major histocompatibility complex, class II, DQ alpha 1
## 19348                                                                     major histocompatibility complex, class II, DQ alpha 1
## 19349                                                                     major histocompatibility complex, class II, DQ alpha 1
## 19350                                                                     major histocompatibility complex, class II, DQ alpha 1
## 19351                                                                     major histocompatibility complex, class II, DQ alpha 1
## 19352                                                                     major histocompatibility complex, class II, DQ alpha 1
## 19353                                                                     major histocompatibility complex, class II, DQ alpha 1
## 19354                                                                     major histocompatibility complex, class II, DQ alpha 1
## 19355                                                                     major histocompatibility complex, class II, DQ alpha 1
## 19356                                                                     major histocompatibility complex, class II, DQ alpha 1
## 19357                                                                     major histocompatibility complex, class II, DQ alpha 1
## 19359                                                                      major histocompatibility complex, class II, DQ beta 1
## 19360                                                                      major histocompatibility complex, class II, DQ beta 1
## 19361                                                                      major histocompatibility complex, class II, DQ beta 1
## 19362                                                                      major histocompatibility complex, class II, DQ beta 1
## 19363                                                                      major histocompatibility complex, class II, DQ beta 1
## 19364                                                                      major histocompatibility complex, class II, DQ beta 1
## 19366                                                                                                   HLA-DQB1 antisense RNA 1
## 19367                                                                                                   HLA-DQB1 antisense RNA 1
## 19368                                                                                                   HLA-DQB1 antisense RNA 1
## 19369                                                                                                   HLA-DQB1 antisense RNA 1
## 19370                                                                                                   HLA-DQB1 antisense RNA 1
## 19371                                                                                                   HLA-DQB1 antisense RNA 1
## 19377                                                                     major histocompatibility complex, class II, DQ alpha 2
## 19378                                                                     major histocompatibility complex, class II, DQ alpha 2
## 19379                                                                     major histocompatibility complex, class II, DQ alpha 2
## 19380                                                                     major histocompatibility complex, class II, DQ alpha 2
## 19381                                                                     major histocompatibility complex, class II, DQ alpha 2
## 19382                                                                     major histocompatibility complex, class II, DQ alpha 2
## 19383                                                                     major histocompatibility complex, class II, DQ alpha 2
## 19386                                                                      major histocompatibility complex, class II, DQ beta 2
## 19387                                                                      major histocompatibility complex, class II, DQ beta 2
## 19388                                                                      major histocompatibility complex, class II, DQ beta 2
## 19389                                                                      major histocompatibility complex, class II, DQ beta 2
## 19390                                                                      major histocompatibility complex, class II, DQ beta 2
## 19391                                                                      major histocompatibility complex, class II, DQ beta 2
## 19392                                                                      major histocompatibility complex, class II, DQ beta 2
## 19394                                                                        major histocompatibility complex, class II, DO beta
## 19395                                                                        major histocompatibility complex, class II, DO beta
## 19396                                                                        major histocompatibility complex, class II, DO beta
## 19397                                                                        major histocompatibility complex, class II, DO beta
## 19398                                                                        major histocompatibility complex, class II, DO beta
## 19400                                                                     transporter 2, ATP binding cassette subfamily B member
## 19401                                                                     transporter 2, ATP binding cassette subfamily B member
## 19402                                                                     transporter 2, ATP binding cassette subfamily B member
## 19403                                                                     transporter 2, ATP binding cassette subfamily B member
## 19404                                                                     transporter 2, ATP binding cassette subfamily B member
## 19405                                                                     transporter 2, ATP binding cassette subfamily B member
## 19406                                                                     transporter 2, ATP binding cassette subfamily B member
## 19408                                                                                              proteasome 20S subunit beta 8
## 19409                                                                                              proteasome 20S subunit beta 8
## 19410                                                                                              proteasome 20S subunit beta 8
## 19411                                                                                              proteasome 20S subunit beta 8
## 19412                                                                                              proteasome 20S subunit beta 8
## 19413                                                                                              proteasome 20S subunit beta 8
## 19414                                                                                              proteasome 20S subunit beta 8
## 19417                                                                                              proteasome 20S subunit beta 9
## 19418                                                                                              proteasome 20S subunit beta 9
## 19419                                                                                              proteasome 20S subunit beta 9
## 19420                                                                                              proteasome 20S subunit beta 9
## 19421                                                                                              proteasome 20S subunit beta 9
## 19422                                                                                              proteasome 20S subunit beta 9
## 19423                                                                                              proteasome 20S subunit beta 9
## 19425                                                                     transporter 1, ATP binding cassette subfamily B member
## 19426                                                                     transporter 1, ATP binding cassette subfamily B member
## 19427                                                                     transporter 1, ATP binding cassette subfamily B member
## 19428                                                                     transporter 1, ATP binding cassette subfamily B member
## 19429                                                                     transporter 1, ATP binding cassette subfamily B member
## 19430                                                                     transporter 1, ATP binding cassette subfamily B member
## 19431                                                                     transporter 1, ATP binding cassette subfamily B member
## 19435                                                                        major histocompatibility complex, class II, DM beta
## 19436                                                                        major histocompatibility complex, class II, DM beta
## 19437                                                                        major histocompatibility complex, class II, DM beta
## 19438                                                                        major histocompatibility complex, class II, DM beta
## 19439                                                                        major histocompatibility complex, class II, DM beta
## 19440                                                                        major histocompatibility complex, class II, DM beta
## 19441                                                                        major histocompatibility complex, class II, DM beta
## 19445                                                                       major histocompatibility complex, class II, DM alpha
## 19446                                                                       major histocompatibility complex, class II, DM alpha
## 19447                                                                       major histocompatibility complex, class II, DM alpha
## 19448                                                                       major histocompatibility complex, class II, DM alpha
## 19449                                                                       major histocompatibility complex, class II, DM alpha
## 19450                                                                       major histocompatibility complex, class II, DM alpha
## 19451                                                                       major histocompatibility complex, class II, DM alpha
## 19453                                                                                                   bromodomain containing 2
## 19454                                                                                                   bromodomain containing 2
## 19455                                                                                                   bromodomain containing 2
## 19456                                                                                                   bromodomain containing 2
## 19457                                                                                                   bromodomain containing 2
## 19458                                                                                                   bromodomain containing 2
## 19462                                                                       major histocompatibility complex, class II, DO alpha
## 19463                                                                       major histocompatibility complex, class II, DO alpha
## 19464                                                                       major histocompatibility complex, class II, DO alpha
## 19465                                                                       major histocompatibility complex, class II, DO alpha
## 19466                                                                       major histocompatibility complex, class II, DO alpha
## 19467                                                                       major histocompatibility complex, class II, DO alpha
## 19469                                                                     major histocompatibility complex, class II, DP alpha 1
## 19470                                                                     major histocompatibility complex, class II, DP alpha 1
## 19471                                                                     major histocompatibility complex, class II, DP alpha 1
## 19472                                                                     major histocompatibility complex, class II, DP alpha 1
## 19473                                                                     major histocompatibility complex, class II, DP alpha 1
## 19474                                                                     major histocompatibility complex, class II, DP alpha 1
## 19475                                                                     major histocompatibility complex, class II, DP alpha 1
## 19477                                                                      major histocompatibility complex, class II, DP beta 1
## 19478                                                                      major histocompatibility complex, class II, DP beta 1
## 19479                                                                      major histocompatibility complex, class II, DP beta 1
## 19480                                                                      major histocompatibility complex, class II, DP beta 1
## 19481                                                                      major histocompatibility complex, class II, DP beta 1
## 19482                                                                      major histocompatibility complex, class II, DP beta 1
## 19483                                                                      major histocompatibility complex, class II, DP beta 1
## 19488                                                         major histocompatibility complex, class II, DP beta 2 (pseudogene)
## 19489                                                         major histocompatibility complex, class II, DP beta 2 (pseudogene)
## 19490                                                         major histocompatibility complex, class II, DP beta 2 (pseudogene)
## 19491                                                         major histocompatibility complex, class II, DP beta 2 (pseudogene)
## 19492                                                         major histocompatibility complex, class II, DP beta 2 (pseudogene)
## 19493                                                         major histocompatibility complex, class II, DP beta 2 (pseudogene)
## 19494                                                         major histocompatibility complex, class II, DP beta 2 (pseudogene)
## 19498                                                                                             collagen type XI alpha 2 chain
## 19499                                                                                             collagen type XI alpha 2 chain
## 19500                                                                                             collagen type XI alpha 2 chain
## 19501                                                                                             collagen type XI alpha 2 chain
## 19502                                                                                             collagen type XI alpha 2 chain
## 19503                                                                                             collagen type XI alpha 2 chain
## 19505                                                                                                   retinoid X receptor beta
## 19506                                                                                                   retinoid X receptor beta
## 19507                                                                                                   retinoid X receptor beta
## 19508                                                                                                   retinoid X receptor beta
## 19509                                                                                                   retinoid X receptor beta
## 19512                                                                                          solute carrier family 39 member 7
## 19513                                                                                          solute carrier family 39 member 7
## 19514                                                                                          solute carrier family 39 member 7
## 19515                                                                                          solute carrier family 39 member 7
## 19516                                                                                          solute carrier family 39 member 7
## 19518                                                                                     hydroxysteroid 17-beta dehydrogenase 8
## 19519                                                                                     hydroxysteroid 17-beta dehydrogenase 8
## 19520                                                                                     hydroxysteroid 17-beta dehydrogenase 8
## 19521                                                                                     hydroxysteroid 17-beta dehydrogenase 8
## 19522                                                                                     hydroxysteroid 17-beta dehydrogenase 8
## 19525                                                                                                      ring finger protein 1
## 19526                                                                                                      ring finger protein 1
## 19527                                                                                                      ring finger protein 1
## 19528                                                                                                      ring finger protein 1
## 19529                                                                                                      ring finger protein 1
## 19534                                                                                                       HLA complex group 25
## 19535                                                                                                       HLA complex group 25
## 19536                                                                                                       HLA complex group 25
## 19537                                                                                                       HLA complex group 25
## 19538                                                                                                       HLA complex group 25
## 19539                                                                                                       HLA complex group 25
## 19541                                                                                              VPS52 subunit of GARP complex
## 19542                                                                                              VPS52 subunit of GARP complex
## 19543                                                                                              VPS52 subunit of GARP complex
## 19544                                                                                              VPS52 subunit of GARP complex
## 19545                                                                                              VPS52 subunit of GARP complex
## 19546                                                                                              VPS52 subunit of GARP complex
## 19548                                                                                                      ribosomal protein S18
## 19549                                                                                                      ribosomal protein S18
## 19550                                                                                                      ribosomal protein S18
## 19551                                                                                                      ribosomal protein S18
## 19552                                                                                                      ribosomal protein S18
## 19554                                                                                           beta-1,3-galactosyltransferase 4
## 19555                                                                                           beta-1,3-galactosyltransferase 4
## 19556                                                                                           beta-1,3-galactosyltransferase 4
## 19557                                                                                           beta-1,3-galactosyltransferase 4
## 19559                                                                                                        WD repeat domain 46
## 19560                                                                                                        WD repeat domain 46
## 19561                                                                                                        WD repeat domain 46
## 19562                                                                                                        WD repeat domain 46
## 19564                                                                                                        prefoldin subunit 6
## 19565                                                                                                        prefoldin subunit 6
## 19566                                                                                                        prefoldin subunit 6
## 19567                                                                                                        prefoldin subunit 6
## 19569                                                                      ral guanine nucleotide dissociation stimulator like 2
## 19570                                                                      ral guanine nucleotide dissociation stimulator like 2
## 19571                                                                      ral guanine nucleotide dissociation stimulator like 2
## 19572                                                                      ral guanine nucleotide dissociation stimulator like 2
## 19574                                                                                                        TAP binding protein
## 19575                                                                                                        TAP binding protein
## 19576                                                                                                        TAP binding protein
## 19577                                                                                                        TAP binding protein
## 19579                                                                                   zinc finger and BTB domain containing 22
## 19580                                                                                   zinc finger and BTB domain containing 22
## 19581                                                                                   zinc finger and BTB domain containing 22
## 19582                                                                                   zinc finger and BTB domain containing 22
## 19584                                                                                            death domain associated protein
## 19585                                                                                            death domain associated protein
## 19586                                                                                            death domain associated protein
## 19587                                                                                            death domain associated protein
## 19588                                                                                            death domain associated protein
## 19593                                                                                                   kinesin family member C1
## 19594                                                                                                   kinesin family member C1
## 19595                                                                                                   kinesin family member C1
## 19598                                                                                                       PHD finger protein 1
## 19599                                                                                                       PHD finger protein 1
## 19601                                                                                     cutA divalent cation tolerance homolog
## 19603                                                                                   synaptic Ras GTPase activating protein 1
## 19606                                                                                    zinc finger and BTB domain containing 9
## 19712                                                                                                  transmembrane protein 217
## 20008                                                                             RNA component of 7SK nuclear ribonucleoprotein
## 20117                                                                                           protein tyrosine phosphatase 4A1
## 20315                                                                                        inhibitor of Bruton tyrosine kinase
## 20319                                                                                                   trophoblast glycoprotein
## 20429                                                                                                       midasin AAA ATPase 1
## 20434                                                                                             caspase 8 associated protein 2
## 20438                                                                                              gap junction protein alpha 10
## 20853                                                                                                       SOGA family member 3
## 20861                                                                                             thymocyte selection associated
## 20863                                                                               protein tyrosine phosphatase receptor type K
## 21153                                                                     TGF-beta activated kinase 1 (MAP3K7) binding protein 2
## 21178                                                                                          retinoic acid early transcript 1E
## 21180                                                                                                     RAET1E antisense RNA 1
## 21477                                                                                     ER membrane associated RNA degradation
## 21480                                                                                 long intergenic non-protein coding RNA 242
## 21482                                                                                 long intergenic non-protein coding RNA 574
## 21491                                                                                        delta like canonical Notch ligand 1
## 21493                                                                                       family with sequence similarity 120B
## 21498                                                                                              proteasome 20S subunit beta 1
## 21515                                                                           FAM20C golgi associated secretory pathway kinase
## 21516                                                                           FAM20C golgi associated secretory pathway kinase
## 21517                                                                           FAM20C golgi associated secretory pathway kinase
## 21606                                                                                               Miyoshi muscular dystrophy 2
## 21982                                                                                                                 chimerin 2
## 22711                                                                                             tripartite motif containing 74
## 22826                                                                                               deltex E3 ubiquitin ligase 2
## 22830                                                                                                               uroplakin 3B
## 22836                                                                                                      POM121 and ZP3 fusion
## 23113                                                                                SMAD specific E3 ubiquitin protein ligase 1
## 23115                                                                                                karyopherin subunit alpha 7
## 23300                                                                                             armadillo repeat containing 10
## 23303                                                                            N-acyl phosphatidylethanolamine phospholipase D
## 23307                                                                                                       DPY19L2 pseudogene 2
## 23359                                                              protein kinase cAMP-dependent type II regulatory subunit beta
## 23362                                                                                             HMG-box transcription factor 1
## 23365                                                                                    component of oligomeric golgi complex 5
## 23369                                                                                              G protein-coupled receptor 22
## 23371                                                                                             dihydrouridine synthase 4 like
## 23374                                                                                      B cell receptor associated protein 29
## 23865                                                                                                        acylglycerol kinase
## 23870                                                                                                       WEE2 antisense RNA 1
## 23872                                                                                      WEE2 oocyte meiosis inhibiting kinase
## 23875                                                                                      single stranded DNA binding protein 1
## 23889                                                                                                       maltase-glucoamylase
## 23897                                                                                                         serine protease 58
## 23943                                                                                                MT-RNR2 like 6 (pseudogene)
## 23953                                                                                                          serine protease 1
## 23968                                                                                                            EPH receptor B6
## 23970                                                           transient receptor potential cation channel subfamily V member 6
## 23973                                                           transient receptor potential cation channel subfamily V member 5
## 23976                                                                              Kell metallo-endopeptidase (Kell blood group)
## 23978                                                                           olfactory receptor family 9 subfamily A member 2
## 23981                                                                           olfactory receptor family 6 subfamily V member 1
## 23999                                                                                                                      zyxin
## 24001                                                                                                            EPH receptor A1
## 24003                                                                                                      EPHA1 antisense RNA 1
## 24006                                                                                                 taste 2 receptor member 60
## 24008                                                                                                 taste 2 receptor member 41
## 24014                                                                                                     CTAGE family member 15
## 24023                                                                                                      CTAGE family member 6
## 24028                                                                           olfactory receptor family 2 subfamily F member 2
## 24031                                                                           olfactory receptor family 2 subfamily F member 1
## 24036                                                                           olfactory receptor family 6 subfamily B member 1
## 24038                                                                           olfactory receptor family 2 subfamily A member 5
## 24040                                                                          olfactory receptor family 2 subfamily A member 25
## 24043                                                                          olfactory receptor family 2 subfamily A member 12
## 24045                                                                           olfactory receptor family 2 subfamily A member 2
## 24048                                                                          olfactory receptor family 2 subfamily A member 14
## 24054                                                                                                      CTAGE family member 4
## 24056                                                                                  Rho guanine nucleotide exchange factor 35
## 24059                                                                          olfactory receptor family 2 subfamily A member 42
## 24063                                                                           olfactory receptor family 2 subfamily A member 7
## 24065                                                                                                      CTAGE family member 8
## 24069                                                                           olfactory receptor family 2 subfamily A member 1
## 24071                                                                                   Rho guanine nucleotide exchange factor 5
## 24073                                                                                                   NOBOX oogenesis homeobox
## 24087                                                                                             contactin associated protein 2
## 24294                                                                              protein tyrosine phosphatase receptor type N2
## 24318                                                                           protein phosphatase 2 regulatory subunit B''beta
## 24319                                                                           protein phosphatase 2 regulatory subunit B''beta
## 24987                                                                                                              G antigen 12I
## 25479                                                                                              T-box transcription factor 22
## 25740                                                                                          RAB9B, member RAS oncogene family
## 25746                                                                                                          thymosin beta 15B
## 25977                                                                                     MCTS1 re-initiation and release factor
## 25979                                                                                               C1GALT1 specific chaperone 1
## 25983                                                                                  cancer/testis antigen family 47 member B1
## 25988                                                                                 cancer/testis antigen family 47 member A11
## 25989                                                                                 cancer/testis antigen family 47 member A11
## 26001                                                                                  cancer/testis antigen family 47 member A6
## 26005                                                                                  cancer/testis antigen family 47 member A4
## 26010                                                                                  cancer/testis antigen family 47 member A1
## 26016                                                                                                  glutamate dehydrogenase 2
## 26624                                                                                DEAD/H-box helicase 11 like 16 (pseudogene)
## 26625                                                                                DEAD/H-box helicase 11 like 16 (pseudogene)
## 26626                                                                                DEAD/H-box helicase 11 like 16 (pseudogene)
## 26648                                                                                                           glutamate rich 1
## 26656                                                                                                   DLG associated protein 2
## 26657                                                                                                   DLG associated protein 2
## 26658                                                                                                   DLG associated protein 2
## 26659                                                                                                   DLG associated protein 2
## 26663                                                                                    CLN8 transmembrane ER and ERGIC protein
## 26667                                                                                  Rho guanine nucleotide exchange factor 10
## 26669                                                                                           KBTBD11 overlapping transcript 1
## 26670                                                                                           KBTBD11 overlapping transcript 1
## 26673                                                                                  kelch repeat and BTB domain containing 11
## 26677                                                                                                                 myomesin 2
## 26700                                                                                                            microcephalin 1
## 26707                                                                             1-acylglycerol-3-phosphate O-acyltransferase 5
## 26709                                                                                                             microRNA 4659b
## 26711                                                                                                               XK related 5
## 26713                                                                                               uncharacterized LOC100652791
## 26715                                                                                                            defensin beta 1
## 26718                                                                                                           defensin alpha 6
## 26721                                                                                                           defensin alpha 4
## 26723                                                                                               defensin alpha 8, pseudogene
## 26725                                                                                               defensin alpha 9, pseudogene
## 26727                                                                                              defensin alpha 10, pseudogene
## 26729                                                                                                           defensin alpha 1
## 26732                                                                                                          defensin alpha 1B
## 26734                                                                                             defensin theta 1, pseudogene 2
## 26736                                                                                                           defensin alpha 3
## 26740                                                                                                           defensin alpha 5
## 26762                                                                       ubiquitin specific peptidase 17 like family member 4
## 26765                                                                                                   zinc finger protein 705G
## 26766                                                                                                   zinc finger protein 705G
## 26769                                                                                                           defensin beta 4B
## 26770                                                                                                           defensin beta 4B
## 26771                                                                                                           defensin beta 4B
## 26772                                                                                                           defensin beta 4B
## 26775                                                                                                         defensin beta 103B
## 26776                                                                                                         defensin beta 103B
## 26777                                                                                                         defensin beta 103B
## 26779                                                                                               sperm associated antigen 11B
## 26780                                                                                               sperm associated antigen 11B
## 26783                                                                                                         defensin beta 104B
## 26784                                                                                                         defensin beta 104B
## 26786                                                                                                         defensin beta 106B
## 26787                                                                                                         defensin beta 106B
## 26789                                                                                                         defensin beta 105B
## 26790                                                                                                         defensin beta 105B
## 26791                                                                                                         defensin beta 105B
## 26793                                                                                                         defensin beta 107B
## 26794                                                                                                         defensin beta 107B
## 26795                                                                                                         defensin beta 107B
## 26796                                                                                                         defensin beta 107B
## 26818                                                                                                         defensin beta 107A
## 26819                                                                                                         defensin beta 107A
## 26820                                                                                                         defensin beta 107A
## 26821                                                                                                         defensin beta 107A
## 26823                                                                                                         defensin beta 105A
## 26824                                                                                                         defensin beta 105A
## 26825                                                                                                         defensin beta 105A
## 26827                                                                                                         defensin beta 106A
## 26829                                                                                                         defensin beta 104A
## 26831                                                                                               sperm associated antigen 11A
## 26834                                                                                                         defensin beta 103A
## 26835                                                                                                         defensin beta 103A
## 26838                                                                                                           defensin beta 4A
## 26839                                                                                                           defensin beta 4A
## 26840                                                                                                           defensin beta 4A
## 26841                                                                                                           defensin beta 4A
## 26843                                                                                                   zinc finger protein 705B
## 26848                                                                       ubiquitin specific peptidase 17 like family member 8
## 26849                                                                       ubiquitin specific peptidase 17 like family member 8
## 26851                                                                       ubiquitin specific peptidase 17 like family member 3
## 26867                                                                    family with sequence similarity 86, member A pseudogene
## 26878                                                                                                                 claudin 23
## 26882                                                                          multifunctional ROCO family signaling regulator 1
## 26888                                                                                                              microRNA 4660
## 26891                                                                                protein phosphatase 1 regulatory subunit 3B
## 26906                                                                                                                  tankyrase
## 26909                                                                                                               microRNA 597
## 26913                                                                                           methionine sulfoxide reductase A
## 26923                                                                                                         serine protease 55
## 26926                                                                                                              microRNA 4286
## 26928                                                                                         chromosome 8 open reading frame 74
## 26931                                                                                             SRY-box transcription factor 7
## 26934                                                                            PIN2 (TERF1) interacting telomerase inhibitor 1
## 26935                                                                            PIN2 (TERF1) interacting telomerase inhibitor 1
## 26939                                                                                                               microRNA 598
## 26952                                                                                             myotubularin related protein 9
## 26955                                                                                         solute carrier family 35 member G5
## 26957                                                                                     L-threonine dehydrogenase (pseudogene)
## 26964                                                                             BLK proto-oncogene, Src family tyrosine kinase
## 26971                                                                                                     GATA binding protein 4
## 26976                                                                                 farnesyl-diphosphate farnesyltransferase 1
## 26979                                                                                                                cathepsin B
## 26985                                                                                                          defensin beta 136
## 26987                                                                                                          defensin beta 135
## 26989                                                                                                          defensin beta 134
## 27000                                                                                                   zinc finger protein 705D
## 27004                                                                       ubiquitin specific peptidase 17 like family member 7
## 27006                                                                       ubiquitin specific peptidase 17 like family member 2
## 27027                                                                               family with sequence similarity 86 member B2
## 27042                                                                                                           microRNA 5692a-2
## 27044                                                                          LON peptidase N-terminal domain and ring finger 1
## 27046                                                                                                            microRNA 3926-2
## 27049                                                                                 long intergenic non-protein coding RNA 681
## 27055                                                                                         DLC1 Rho GTPase activating protein
## 27502                                                                                             ADAM metallopeptidase domain 9
## 27504                                                                                            ADAM metallopeptidase domain 32
## 27513                                                                                            ADAM metallopeptidase domain 18
## 27515                                                                                             ADAM metallopeptidase domain 2
## 27781                                                                                 long intergenic non-protein coding RNA 588
## 28771                                                                                                                gasdermin C
## 28871                                                                                              G protein-coupled receptor 20
## 28874                                                                                           protein tyrosine phosphatase 4A3
## 28876                                                                 maestro heat like repeat family member 5 (gene/pseudogene)
## 28913                                                                                       lymphocyte antigen 6 family member E
## 28919                                                                                       lymphocyte antigen 6 family member H
## 28935                                                                                         zinc finger CCCH-type containing 3
## 28938                                                                                                                gasdermin D
## 28940                                                                                   maestro heat like repeat family member 6
## 28945                                                                           eukaryotic translation elongation factor 1 delta
## 28947                                                                                      tigger transposable element derived 5
## 28953                                                                                                    zinc finger protein 623
## 28956                                                                                                    zinc finger protein 707
## 28959                                                                                          coiled-coil domain containing 166
## 28962                                                                                        mitogen-activated protein kinase 15
## 28965                                                                                family with sequence similarity 83 member H
## 28971                                                                                      scribble planar cell polarity protein
## 28974                                                                                         poly(U) binding splicing factor 60
## 29003                                                                                           BOP1 ribosomal biogenesis factor
## 29006                                                                                          heat shock transcription factor 1
## 29009                                                                                         diacylglycerol O-acyltransferase 1
## 29011                                                                                 scratch family transcriptional repressor 1
## 29013                                                                                                  transmembrane protein 249
## 29015                                                                                          solute carrier family 52 member 2
## 29017                                                                                    F-box and leucine rich repeat protein 6
## 29019                                                                                            aarF domain containing kinase 5
## 29021                                                                             cleavage and polyadenylation specific factor 1
## 29023                                                                                                               microRNA 939
## 29025                                                                                                              microRNA 1234
## 29028                                                                                          solute carrier family 39 member 4
## 29030                                                                                                   VPS28 subunit of ESCRT-I
## 29056                                                                                                    zinc finger protein 251
## 29074                                                                                 DEAD/H-box helicase 11 like 5 (pseudogene)
## 29075                                                                                 DEAD/H-box helicase 11 like 5 (pseudogene)
## 29218                                                                               protein tyrosine phosphatase receptor type D
## 29664                                                                                                           F-box protein 10
## 30048                                                                   amyloid beta precursor protein binding family A member 1
## 30057                                                                                                    MAM domain containing 2
## 30261                                                                                               SPATA31 subfamily C member 1
## 30430                                                                                         solute carrier family 35 member D2
## 30531                                                                                 bile acid-CoA:amino acid N-acyltransferase
## 30957                                                                  ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 6
## 31129                                                                                                 odorant binding protein 2B
## 31135                                                                                                                  surfeit 6
## 31137                                                                                                mediator complex subunit 22
## 31140                                                                                                      ribosomal protein L7a
## 31142                                                                                            small nucleolar RNA, C/D box 24
## 31145                                                                                           small nucleolar RNA, C/D box 36A
## 31147                                                                                           small nucleolar RNA, C/D box 36C
## 31149                                                                                 SURF1 cytochrome c oxidase assembly factor
## 31151                                                                                                                  surfeit 2
## 31153                                                                                                                  surfeit 4
## 31156                                                                                            REX4 homolog, 3'-5' exonuclease
## 31158                                                                  ADAM metallopeptidase with thrombospondin type 1 motif 13
## 31160                                                                                 calcium channel flower domain containing 1
## 31162                                                                                           solute carrier family 2 member 6
## 31756                                                                              patched domain containing 3 (gene/pseudogene)
## 31939                                                                        hydroxysteroid 17-beta dehydrogenase 7 pseudogene 2
## 32044                                                                          olfactory receptor family 13 subfamily A member 1
## 32046                                                                                                arachidonate 5-lipoxygenase
## 32135                                                                                family with sequence similarity 25 member C
## 32485                                                                                          DNAJC9 and MRPS16 antisense RNA 1
## 32523                                                                                     N-deacetylase and N-sulfotransferase 2
## 32545                                                                                                lysine acetyltransferase 6B
## 32590                                                                                       discs large MAGUK scaffold protein 5
## 32755                                                                                      ATPase family AAA domain containing 1
## 32757                                                                                                     cofilin 1 pseudogene 1
## 32760                                                                            killin, p53 regulated DNA replication inhibitor
## 32762                                                                                             phosphatase and tensin homolog
## 33559                                                                                              phosphatidylserine synthase 2
## 33562                                                                                        ribonuclease/angiogenin inhibitor 1
## 33565                                                                                                HRas proto-oncogene, GTPase
## 33567                                                                                          leucine rich repeat containing 56
## 33571                                                                                     Ras association domain family member 7
## 33573                                                                                                           MIR210 host gene
## 33576                                                                                              PHD and ring finger domains 1
## 33578                                                                                             interferon regulatory factor 7
## 33580                                                                                           cadherin related family member 5
## 33582                                                                                                                   secretin
## 33584                                                                                                       dopamine receptor D4
## 33586                                                                                                 DEAF1 transcription factor
## 33610                                                                          adaptor related protein complex 2 subunit alpha 2
## 33611                                                                          adaptor related protein complex 2 subunit alpha 2
## 33615                                                                                      mucin 6, oligomeric mucus/gel-forming
## 33616                                                                                      mucin 6, oligomeric mucus/gel-forming
## 33617                                                                                      mucin 6, oligomeric mucus/gel-forming
## 33620                                                                                      mucin 2, oligomeric mucus/gel-forming
## 33621                                                                                      mucin 2, oligomeric mucus/gel-forming
## 33623                                                                                    mucin 5AC, oligomeric mucus/gel-forming
## 33632                                                                                             dual specificity phosphatase 8
## 33633                                                                                             dual specificity phosphatase 8
## 33635                                                                                          KRTAP5-1/KRTAP5-2 antisense RNA 1
## 33636                                                                                          KRTAP5-1/KRTAP5-2 antisense RNA 1
## 33638                                                                                             keratin associated protein 5-1
## 33639                                                                                             keratin associated protein 5-1
## 33641                                                                                             keratin associated protein 5-2
## 33642                                                                                             keratin associated protein 5-2
## 33644                                                                                             keratin associated protein 5-3
## 33645                                                                                             keratin associated protein 5-3
## 33647                                                                                             keratin associated protein 5-4
## 33648                                                                                             keratin associated protein 5-4
## 33650                                                                                             keratin associated protein 5-5
## 33651                                                                                             keratin associated protein 5-5
## 33654                                                                                family with sequence similarity 99 member A
## 33655                                                                                family with sequence similarity 99 member A
## 33658                                                                                family with sequence similarity 99 member B
## 33659                                                                                family with sequence similarity 99 member B
## 33662                                                                                             keratin associated protein 5-6
## 33664                                                                                interferon induced transmembrane protein 10
## 33674                                                                                                            synaptotagmin 8
## 33676                                                                                            troponin I2, fast skeletal type
## 33678                                                                                              lymphocyte specific protein 1
## 33680                                                                                                              microRNA 4298
## 33685                                                                                            troponin T3, fast skeletal type
## 33688                                                                                        mitochondrial ribosomal protein L23
## 33690                                                                                                     MRPL23 antisense RNA 1
## 33693                                                                              H19 imprinted maternally expressed transcript
## 33697                                                                                                       INS-IGF2 readthrough
## 33714                                                                       potassium voltage-gated channel subfamily Q member 1
## 33718                                                                                                      KCNQ1 antisense RNA 1
## 33720                                                                                                  KCNQ1 downstream neighbor
## 33722                                                                                       cyclin dependent kinase inhibitor 1C
## 33725                                                                                         solute carrier family 22 member 18
## 33727                                                                          pleckstrin homology like domain family A member 2
## 33729                                                                                       nucleosome assembly protein 1 like 4
## 33731                                                                                          small nucleolar RNA, H/ACA box 54
## 33853                                                                                              hypophosphatemic bone disease
## 33983                                                                           olfactory receptor family 5 subfamily P member 2
## 33984                                                                           olfactory receptor family 5 subfamily P member 2
## 33986                                                                           olfactory receptor family 5 subfamily P member 3
## 33987                                                                           olfactory receptor family 5 subfamily P member 3
## 33991                                                        olfactory receptor family 10 subfamily A member 6 (gene/pseudogene)
## 33992                                                        olfactory receptor family 10 subfamily A member 6 (gene/pseudogene)
## 33994                                                                          olfactory receptor family 10 subfamily A member 3
## 33995                                                                          olfactory receptor family 10 subfamily A member 3
## 33997                                                                                      NLR family pyrin domain containing 10
## 33998                                                                                      NLR family pyrin domain containing 10
## 34197                                                                                                           serum amyloid A1
## 34200                                                                HPS5 biogenesis of lysosomal organelles complex 2 subunit 2
## 34202                                                                                 general transcription factor IIH subunit 1
## 34204                                                                                                              microRNA 3159
## 34206                                                                                                    lactate dehydrogenase A
## 34608                                                                             NADH:ubiquinone oxidoreductase core subunit S3
## 34610                                                                               protein tyrosine phosphatase mitochondrial 1
## 34612                                                                                   kelch repeat and BTB domain containing 4
## 34615                                                                               family with sequence similarity 180 member B
## 34617                                                                                                      C1q and TNF related 4
## 34619                                                                                                    mitochondrial carrier 2
## 34621                                                                                                    AGBL carboxypeptidase 2
## 34623                                                                                                   formin binding protein 4
## 34693                                                                          olfactory receptor family 4 subfamily C member 12
## 34789                                                                           olfactory receptor family 5 subfamily T member 2
## 34791                                                                           olfactory receptor family 5 subfamily T member 3
## 34793                                                                           olfactory receptor family 5 subfamily T member 1
## 34795                                                                           olfactory receptor family 8 subfamily H member 1
## 34798                                                         olfactory receptor family 8 subfamily K member 3 (gene/pseudogene)
## 34802                                                                           olfactory receptor family 8 subfamily K member 1
## 34805                                                                           olfactory receptor family 8 subfamily J member 1
## 34834                                                                           olfactory receptor family 9 subfamily G member 1
## 34838                                                                           olfactory receptor family 9 subfamily G member 4
## 34991                                                                                             membrane spanning 4-domains A3
## 35092                                                                         terminal uridylyl transferase 1, U6 snRNA-specific
## 35252                                                                                  DNA polymerase alpha 2, accessory subunit
## 35332                                                                                              neuronal PAS domain protein 4
## 35484                                                                                          PTPRF interacting protein alpha 1
## 35488                                                                                                              microRNA 548k
## 35494                                                                                                                  cortactin
## 35546                                                       leucine rich transmembrane and O-methyltransferase domain containing
## 35925                                                                             N-acetylated alpha-linked acidic dipeptidase 2
## 35927                                                                            cysteine and histidine rich domain containing 1
## 36390                                                                                                            forkhead box R1
## 36398                                                                                                      ribosomal protein S25
## 36400                                                                             trafficking protein particle complex subunit 4
## 36403                                                                                          solute carrier family 37 member 4
## 36406                                                                                                     hypoxia up-regulated 1
## 36410                                                                            VPS11 core subunit of CORVET and HOPS complexes
## 36750                                                                               family with sequence similarity 138 member D
## 36752                                                                                          IQ motif and Sec7 domain ArfGEF 3
## 36784                                                                                                              microRNA 3649
## 36786                                                                                                     adiponectin receptor 2
## 36790                                                              calcium voltage-gated channel auxiliary subunit alpha2delta 4
## 36792                                                                           leucine rich repeats and transmembrane domains 2
## 36795                                                                                 long intergenic non-protein coding RNA 940
## 36797                                                                                                          decapping mRNA 1B
## 36799                                                                             calcium voltage-gated channel subunit alpha1 C
## 36803                                                                                              CACNA1C intronic transcript 2
## 36804                                                                                              CACNA1C intronic transcript 2
## 36806                                                                                                    CACNA1C antisense RNA 4
## 36811                                                                                                    CACNA1C antisense RNA 2
## 36813                                                                                                    CACNA1C antisense RNA 1
## 36959                                                                                                             complement C1r
## 36961                                                                                           complement C1r subcomponent like
## 36963                                                                                                       C1RL antisense RNA 1
## 36966                                                                                                  retinol binding protein 5
## 36969                                                                                                              calsyntenin 3
## 36972                                                                                            peroxisomal biogenesis factor 5
## 37000                                                                                     C-type lectin domain family 4 member A
## 37123                                                                                                  taste 2 receptor member 7
## 37124                                                                                                  taste 2 receptor member 7
## 37126                                                                                                  taste 2 receptor member 8
## 37127                                                                                                  taste 2 receptor member 8
## 37129                                                                                                  taste 2 receptor member 9
## 37130                                                                                                  taste 2 receptor member 9
## 37132                                                                                                             proline rich 4
## 37133                                                                                                             proline rich 4
## 37135                                                                                                 taste 2 receptor member 10
## 37136                                                                                                 taste 2 receptor member 10
## 37139                                                                                    proline rich protein HaeIII subfamily 1
## 37140                                                                                    proline rich protein HaeIII subfamily 1
## 37141                                                                                    proline rich protein HaeIII subfamily 1
## 37142                                                                                    proline rich protein HaeIII subfamily 1
## 37145                                                                                                 taste 2 receptor member 13
## 37146                                                                                                 taste 2 receptor member 13
## 37148                                                                                    proline rich protein HaeIII subfamily 2
## 37149                                                                                    proline rich protein HaeIII subfamily 2
## 37151                                                                                                 taste 2 receptor member 14
## 37152                                                                                                 taste 2 receptor member 14
## 37155                                                                                                 taste 2 receptor member 50
## 37156                                                                                                 taste 2 receptor member 50
## 37158                                                                                                 taste 2 receptor member 20
## 37159                                                                                                 taste 2 receptor member 20
## 37161                                                                                                 taste 2 receptor member 19
## 37162                                                                                                 taste 2 receptor member 19
## 37164                                                                                                 taste 2 receptor member 31
## 37165                                                                                                 taste 2 receptor member 31
## 37169                                                                                                 taste 2 receptor member 46
## 37170                                                                                                 taste 2 receptor member 46
## 37173                                                                                                 taste 2 receptor member 43
## 37174                                                                                                 taste 2 receptor member 43
## 37177                                                                                                 taste 2 receptor member 30
## 37178                                                                                                 taste 2 receptor member 30
## 37185                                                                                                 taste 2 receptor member 42
## 37189                                                                                     proline rich protein BstNI subfamily 3
## 37191                                                                                     proline rich protein BstNI subfamily 4
## 37193                                                                                     proline rich protein BstNI subfamily 1
## 37194                                                                                     proline rich protein BstNI subfamily 1
## 37196                                                                                     proline rich protein BstNI subfamily 2
## 37197                                                                                     proline rich protein BstNI subfamily 2
## 37198                                                                                     proline rich protein BstNI subfamily 2
## 37208                                                                                                               BCL2 like 14
## 37211                                                                                             LDL receptor related protein 6
## 37217                                                                                                  MANSC domain containing 1
## 37220                                                                          loss of heterozygosity on chromosome 12, region 2
## 37224                                                                                            dual specificity phosphatase 16
## 38017                                                                                                                homeobox C5
## 38626                                                                                                      MGAT4 family member C
## 38627                                                                                                      MGAT4 family member C
## 38836                                                                                                                anoctamin 4
## 38841                                                                                           solute carrier family 5 member 8
## 39280                                                                             BAF chromatin remodeling complex subunit BCL7A
## 39283                                                                                                    MLX interacting protein
## 39342                                                                                             dynein axonemal heavy chain 10
## 39344                                                                                           coiled-coil domain containing 92
## 39443                                                                                    piwi like RNA-mediated gene silencing 1
## 39488                                                                                                       DEAD-box helicase 51
## 39490                                                                                     nucleolar complex associated 4 homolog
## 39494                                                                            polypeptide N-acetylgalactosaminyltransferase 9
## 39684                                                                                              spermatogenesis associated 13
## 39685                                                                                              spermatogenesis associated 13
## 40164                                                                          heterogeneous nuclear ribonucleoprotein A1 like 2
## 40567                                                                                                      NALCN antisense RNA 1
## 40674                                                                                long intergenic non-protein coding RNA 1043
## 40676                                                                                long intergenic non-protein coding RNA 1044
## 40678                                                                                                sperm acrosome associated 7
## 40680                                                                                 tubulin gamma complex associated protein 3
## 40711                                                                                     ATPase H+/K+ transporting subunit beta
## 40713                                                                                        G protein-coupled receptor kinase 1
## 40714                                                                                        G protein-coupled receptor kinase 1
## 40716                                                                                 long intergenic non-protein coding RNA 552
## 40717                                                                                 long intergenic non-protein coding RNA 552
## 40719                                                                                                 transmembrane protein 255B
## 40728                                                                                                RAS p21 protein activator 3
## 41139                                                                                                      DHRS4 antisense RNA 1
## 41141                                                                                                  dehydrogenase/reductase 4
## 41146                                                                                                                   copine 6
## 41148                                                                                               neural retina leucine zipper
## 41150                                                                         phosphoenolpyruvate carboxykinase 2, mitochondrial
## 41152                                                                                         DDB1 and CUL4 associated factor 11
## 41155                                                                               fat storage inducing transmembrane protein 1
## 41157                                                                                             proteasome activator subunit 1
## 41159                                                                                      ER membrane protein complex subunit 9
## 41162                                                                                             proteasome activator subunit 2
## 41164                                                                                                     ring finger protein 31
## 41168                                                                                             interferon regulatory factor 9
## 41170                                                                                         REC8 meiotic recombination protein
## 41172                                                                                                                 importin 4
## 41175                                                                                       transmembrane 9 superfamily member 1
## 41177                                                                                            testis specific serine kinase 4
## 41179                                                                                     charged multivesicular body protein 4A
## 41182                                                                                          magnesium dependent phosphatase 1
## 41184                                                                                                     NEDD8-MDP1 readthrough
## 41186                                                                                              NEDD8 ubiquitin like modifier
## 41188                                                                                        guanosine monophosphate reductase 2
## 41190                                                                                         TERF1 interacting nuclear factor 2
## 41192                                                                                                         transglutaminase 1
## 41194                                                                                Rab geranylgeranyltransferase subunit alpha
## 41196                                                                                                  dehydrogenase/reductase 1
## 41198                                                                                                     NOP9 nucleolar protein
## 41200                                                                                   cell death inducing DFFA like effector b
## 41202                                                                                                  leukotriene B4 receptor 2
## 41204                                                                                                    leukotriene B4 receptor
## 41206                                                                                                        adenylate cyclase 4
## 41209                                                                             receptor interacting serine/threonine kinase 3
## 41212                                                                                      nuclear factor of activated T cells 4
## 41381                                                                                                    surfactant associated 3
## 41493                                                                                 long intergenic non-protein coding RNA 871
## 41811                                                                                      sphingosine-1-phosphate phosphatase 1
## 41842                                                                                                    CHURC1-FNTB readthrough
## 42016                                                                                                  prostaglandin reductase 2
## 42291                                                                     cation channel sperm associated auxiliary subunit beta
## 42297                                                                                                 tandem C2 domains, nuclear
## 42315                                                                                                             chromogranin A
## 42317                                                                                        inositol-tetrakisphosphate 1-kinase
## 42319                                                                                                      ITPK1 antisense RNA 1
## 42322                                                                                                   modulator of apoptosis 1
## 42324                                                                                                  transmembrane protein 251
## 42328                                                                         ubiquitin protein ligase E3 component n-recognin 7
## 42331                                                                                                    BTB domain containing 7
## 42334                                                                              unc-79 homolog, NALCN channel complex subunit
## 42336                                                                                            cytochrome c oxidase subunit 8C
## 42339                                                                                             proline rich membrane anchor 1
## 42341                                                                                                    FAM181A antisense RNA 1
## 42343                                                                               family with sequence similarity 181 member A
## 42345                                                                                   ankyrin repeat and SOCS box containing 2
## 42350                                                                           OTU deubiquitinase, ubiquitin aldehyde binding 2
## 42352                                                                                                       DEAD-box helicase 24
## 42354                                                                               interferon alpha inducible protein 27 like 1
## 42356                                                                                      interferon alpha inducible protein 27
## 42358                                                                               interferon alpha inducible protein 27 like 2
## 42360                                                                                 protein phosphatase 4 regulatory subunit 4
## 42362                                                                                                  serpin family A member 10
## 42364                                                                                                   serpin family A member 6
## 42367                                                                                                   serpin family A member 1
## 42711                                                                                                  transmembrane protein 179
## 42713                                                                                       chromosome 14 open reading frame 180
## 42827                                                                                ADAM metallopeptidase domain 6 (pseudogene)
## 43003                                                                                       POTE ankyrin domain family member B2
## 43035                                                                                        POTE ankyrin domain family member B
## 43039                                                                                               neurofibromin 1 pseudogene 2
## 43050                                                                           olfactory receptor family 4 subfamily M member 2
## 43052                                                                           olfactory receptor family 4 subfamily N member 4
## 43069                                                                                      golgin A8 family member D, pseudogene
## 43070                                                                                      golgin A8 family member D, pseudogene
## 43071                                                                                      golgin A8 family member D, pseudogene
## 43075                                                                                                    golgin A6 family like 1
## 43076                                                                                                    golgin A6 family like 1
## 43077                                                                                                    golgin A6 family like 1
## 43082                                                                                 tubulin gamma complex associated protein 5
## 43083                                                                                 tubulin gamma complex associated protein 5
## 43085                                                                                     cytoplasmic FMR1 interacting protein 1
## 43086                                                                                     cytoplasmic FMR1 interacting protein 1
## 43089                                                                                               NIPA magnesium transporter 1
## 43105                                                                                      golgin A8 family member E, pseudogene
## 43117                                                                                                    golgin A6 family like 2
## 43122                                                                                                      MAGE family member L2
## 43125                                                                                                 necdin, MAGE family member
## 43251                                                                                     OCA2 melanosomal transmembrane protein
## 43255                                                               HECT and RLD domain containing E3 ubiquitin protein ligase 2
## 43256                                                               HECT and RLD domain containing E3 ubiquitin protein ligase 2
## 43263                                                                                                  golgin A8 family member F
## 43264                                                                                                  golgin A8 family member F
## 43274                                                                                                  golgin A8 family member G
## 43275                                                                                                  golgin A8 family member G
## 43283                                                                                                         HERC2 pseudogene 9
## 43286                                                                                                  golgin A8 family member M
## 43287                                                                                                  golgin A8 family member M
## 43300                                                                   amyloid beta precursor protein binding family A member 2
## 43303                                                                              family with sequence similarity 189 member A1
## 43312                                                                                                   tight junction protein 1
## 43321                                                                                                  golgin A8 family member J
## 43326                                                                                                          ULK4 pseudogene 3
## 43328                                                                                                  golgin A8 family member T
## 43340                                                                           CHRNA7 (exons 5-10) and FAM7A (exons A-E) fusion
## 43351                                                                                                  golgin A8 family member Q
## 43356                                                                                                          ULK4 pseudogene 2
## 43364                                                                                          Rho GTPase activating protein 11B
## 43365                                                                                          Rho GTPase activating protein 11B
## 43366                                                                                          Rho GTPase activating protein 11B
## 43375                                                                                     FANCD2 and FANCI associated nuclease 1
## 43378                                                                                            myotubularin related protein 10
## 43381                                                           transient receptor potential cation channel subfamily M member 1
## 43387                                                                                                     Kruppel like factor 13
## 43393                                                                             cholinergic receptor nicotinic alpha 7 subunit
## 43394                                                                             cholinergic receptor nicotinic alpha 7 subunit
## 43401                                                                                                  golgin A8 family member K
## 43402                                                                                                  golgin A8 family member K
## 43408                                                                                                          ULK4 pseudogene 1
## 43409                                                                                                          ULK4 pseudogene 1
## 43412                                                                                                  golgin A8 family member O
## 43413                                                                                                  golgin A8 family member O
## 43423                                                                                                  golgin A8 family member N
## 43431                                                                                          Rho GTPase activating protein 11A
## 43433                                                                                                            secretogranin V
## 43434                                                                                                            secretogranin V
## 43438                                                                                       gremlin 1, DAN family BMP antagonist
## 43439                                                                                       gremlin 1, DAN family BMP antagonist
## 43659                                                                                          leucine rich repeat containing 57
## 43736                                                                                                             PAT1 homolog 2
## 43738                                                                                                       beta-2-microglobulin
## 43740                                                                                             tripartite motif containing 69
## 43955                                                                                                   zinc finger protein 280D
## 44154                                                                                               multiple EGF like domains 11
## 44337                                                                  immunoglobulin superfamily containing leucine rich repeat
## 44339                                                                        signaling receptor and transporter of retinol STRA6
## 44342                                                                                           coiled-coil domain containing 33
## 44345                                                                             cytochrome P450 family 11 subfamily A member 1
## 44349                                                                              semaphorin 7A (John Milton Hagen blood group)
## 44351                                                                                                           ubiquitin like 7
## 44569                                                                                                   golgin A6 family like 10
## 44570                                                                                                   golgin A6 family like 10
## 44572                                                                                                        UBE2Q2 pseudogene 2
## 44576                                                                                                    golgin A6 family like 9
## 44584                                                                                                      ribosomal protein S17
## 44606                                                                      cytoplasmic polyadenylation element binding protein 1
## 44649                                                                                                    golgin A6 family like 4
## 44650                                                                                                    golgin A6 family like 4
## 44732                                                                                   DET1 partner of COP1 E3 ubiquitin ligase
## 45030                                                                           olfactory receptor family 4 subfamily F member 4
## 45033                                                                               family with sequence similarity 138 member E
## 45035                                                                                                           microRNA 1302-10
## 45038                                                                                 DEAD/H-box helicase 11 like 9 (pseudogene)
## 45071                                                                                                2,4-dienoyl-CoA reductase 2
## 45073                                                                                         RAB11 family interacting protein 3
## 45077                                                                                                                 calpain 15
## 45184                                                                                              meiosis specific with OB-fold
## 45190                                                                           heparan sulfate-glucosamine 3-sulfotransferase 6
## 45278                                                                                                         serine protease 21
## 45281                                                                                                zymogen granule protein 16B
## 45283                                                                                             serine protease 30, pseudogene
## 45285                                                                                                         serine protease 22
## 45324                                                                           olfactory receptor family 1 subfamily F member 1
## 45366                                                                                                  GLIS family zinc finger 2
## 45369                                                                                presequence translocase associated motor 16
## 45372                                                                                                    CORO7-PAM16 readthrough
## 45374                                                                                                                  coronin 7
## 45376                                                                                                                    vasorin
## 45378                                                                           DnaJ heat shock protein family (Hsp40) member A3
## 45380                                                                                                   NmrA like redox sensor 1
## 45382                                                                                                           heme oxygenase 2
## 45384                                                                                           cell death inducing p53 target 1
## 45576                                                                                              poly(A)-specific ribonuclease
## 45581                                                                                           bifunctional apoptosis regulator
## 45584                                                                                                   phospholipase A2 group X
## 45587                                                                  nuclear pore complex interacting protein family member A3
## 45591                                                                  nuclear pore complex interacting protein family member A2
## 45592                                                                  nuclear pore complex interacting protein family member A2
## 45595                                                                     ATP binding cassette subfamily C member 6 pseudogene 2
## 45597                                                                                                          NODAL modulator 1
## 45605                                                                  nuclear pore complex interacting protein family member A1
## 45607                                                                      pyridoxal dependent decarboxylase domain containing 1
## 45612                                                                                              N-terminal asparagine amidase
## 45614                                                                        RRN3 homolog, RNA polymerase I transcription factor
## 45623                                                                  nuclear pore complex interacting protein family member A5
## 45626                                                                            MPV17 mitochondrial inner membrane protein like
## 45627                                                                            MPV17 mitochondrial inner membrane protein like
## 45628                                                                            MPV17 mitochondrial inner membrane protein like
## 45633                                                                                            nudE neurodevelopment protein 1
## 45637                                                                                                      myosin heavy chain 11
## 45645                                                                                  ATP binding cassette subfamily C member 1
## 45648                                                                                  ATP binding cassette subfamily C member 6
## 45651                                                                                                          NODAL modulator 3
## 45662                                                                  nuclear pore complex interacting protein family member A7
## 45671                                                                                                       xylosyltransferase 1
## 45754                                                                                              zona pellucida glycoprotein 2
## 45756                                                                ankyrin repeat and sterile alpha motif domain containing 4B
## 45762                                                                  nuclear pore complex interacting protein family member B3
## 45769                                                                                                   methyltransferase like 9
## 45772                                                                                        immunoglobulin superfamily member 6
## 45783                                                                                                    PDZ domain containing 9
## 45790                                                                                      eukaryotic elongation factor 2 kinase
## 45793                                                                                               RNA polymerase III subunit E
## 45801                                                                  nuclear pore complex interacting protein family member B5
## 45844                                                                                 trinucleotide repeat containing adaptor 6A
## 45847                                                                                          solute carrier family 5 member 11
## 45849                                                                                           Rho GTPase activating protein 17
## 45908                                                                   CLN3 lysosomal/endosomal transmembrane protein, battenin
## 45957                                                                                                       bolA family member 2
## 46515                                                                                            carboxylesterase 1 pseudogene 1
## 46517                                                                                                         carboxylesterase 1
## 46519                                                                                                        carboxylesterase 5A
## 46831                                                                                                          syntrophin beta 2
## 46894                                                                              HYDIN axonemal central pair apparatus protein
## 46903                                                                                                                calbindin 2
## 47003                                                                                                   ZFP1 zinc finger protein
## 47006                                                                                                        chymotrypsinogen B2
## 47008                                                                                                        chymotrypsinogen B1
## 47011                                                                                  BCAR1 scaffold protein, Cas family member
## 47356                                                                                                      double C2 domain beta
## 47359                                                                                     rabphilin 3A like (without C2 domains)
## 47360                                                                                     rabphilin 3A like (without C2 domains)
## 47367                                                                                        chromosome 17 open reading frame 97
## 47371                                                                                              VPS53 subunit of GARP complex
## 47385                                                                                                              nucleoredoxin
## 47386                                                                                                              nucleoredoxin
## 47392                                                                             translocase of inner mitochondrial membrane 22
## 47393                                                                             translocase of inner mitochondrial membrane 22
## 47395                                                                                         ABR activator of RhoGEF and GTPase
## 47396                                                                                         ABR activator of RhoGEF and GTPase
## 47403                                             tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon
## 47411                                                                                          solute carrier family 43 member 2
## 47414                                                                                        scavenger receptor class F member 1
## 47416                                                                                          Rab interacting lysosomal protein
## 47418                                                                                               pre-mRNA processing factor 8
## 47420                                                                                                    TLC domain containing 2
## 47422                                                                                                            MIR22 host gene
## 47424                                                                                                        WD repeat domain 81
## 47427                                                                                                   serpin family F member 2
## 47429                                                                                                   serpin family F member 1
## 47487                                                                           olfactory receptor family 1 subfamily D member 4
## 47657                                                                                         CTD nuclear envelope phosphatase 1
## 47660                                                                              elongator acetyltransferase complex subunit 5
## 47662                                                                                                                  claudin 7
## 47664                                                                                           solute carrier family 2 member 4
## 47667                                                                                                    Y-box binding protein 2
## 47669                                                                                eukaryotic translation initiation factor 5A
## 47671                                                                                             G protein pathway suppressor 2
## 47674                                                                                   neuralized E3 ubiquitin protein ligase 4
## 47677                                                                   ArfGAP with coiled-coil, ankyrin repeat and PH domains 1
## 47679                                                                     potassium channel tetramerization domain containing 11
## 47682                                                                                                   transmembrane protein 95
## 47684                                                                                             tyrosine kinase non receptor 1
## 47688                                                                                                  transmembrane protein 256
## 47690                                                                                                               neuroligin 2
## 47693                                                                                                     spermatid maturation 1
## 47696                                                                                                  transmembrane protein 102
## 47699                                                                                                fibroblast growth factor 11
## 47703                                                                              cholinergic receptor nicotinic beta 1 subunit
## 47705                                                                                    zinc finger and BTB domain containing 4
## 47707                                                                                         solute carrier family 35 member G6
## 47709                                                                                                RNA polymerase II subunit A
## 48022                                                                            LLGL scribble cell polarity complex component 1
## 48024                                                                                              FLII actin remodeling protein
## 48026                                                                                          mitochondrial elongation factor 2
## 48029                                                                                                DNA topoisomerase III alpha
## 48033                                                                                              SMCR8-C9orf72 complex subunit
## 48036                                                                                          serine hydroxymethyltransferase 1
## 48038                                                                                                            envoplakin like
## 48053                                                                                                                galectin 9C
## 48398                                                                                                              myosin XVIIIA
## 48642                                                                                                 matrix metallopeptidase 28
## 48647                                                                              TATA-box binding protein associated factor 15
## 48654                                                                                               C-C motif chemokine ligand 5
## 48659                                                                                                   RAD52 motif containing 1
## 48661                                                                                                            lysozyme like 6
## 48665                                                                                              C-C motif chemokine ligand 16
## 48667                                                                                              C-C motif chemokine ligand 14
## 48671                                                                                              C-C motif chemokine ligand 15
## 48675                                                                                              C-C motif chemokine ligand 23
## 48677                                                                                              C-C motif chemokine ligand 18
## 48678                                                                                              C-C motif chemokine ligand 18
## 48681                                                                                               C-C motif chemokine ligand 3
## 48682                                                                                               C-C motif chemokine ligand 3
## 48684                                                                                               C-C motif chemokine ligand 4
## 48685                                                                                               C-C motif chemokine ligand 4
## 48690                                                                                               TBC1 domain family member 3B
## 48691                                                                                               TBC1 domain family member 3B
## 48692                                                                                               TBC1 domain family member 3B
## 48695                                                                                        C-C motif chemokine ligand 3 like 3
## 48696                                                                                        C-C motif chemokine ligand 3 like 3
## 48697                                                                                        C-C motif chemokine ligand 3 like 3
## 48699                                                                                        C-C motif chemokine ligand 4 like 1
## 48704                                                                                               TBC1 domain family member 3H
## 48706                                                                                        C-C motif chemokine ligand 3 like 1
## 48707                                                                                        C-C motif chemokine ligand 3 like 1
## 48708                                                                                        C-C motif chemokine ligand 3 like 1
## 48710                                                                                        C-C motif chemokine ligand 4 like 2
## 48711                                                                                        C-C motif chemokine ligand 4 like 2
## 48712                                                                                        C-C motif chemokine ligand 4 like 2
## 48714                                                                                               TBC1 domain family member 3G
## 48715                                                                                               TBC1 domain family member 3G
## 48716                                                                                               TBC1 domain family member 3G
## 48717                                                                                               TBC1 domain family member 3G
## 48721                                                                                          zinc finger HIT-type containing 3
## 48724                                                                                                                 myosin XIX
## 48726                                                                    phosphatidylinositol glycan anchor biosynthesis class W
## 48728                                                                                            gametogenetin binding protein 2
## 48731                                                                                                 dehydrogenase/reductase 11
## 48733                                                                                     mitochondrial rRNA methyltransferase 1
## 48739                                                                                                             LIM homeobox 1
## 48742                                                                                apoptosis antagonizing transcription factor
## 48749                                                                                               acetyl-CoA carboxylase alpha
## 48754                                                                                        chromosome 17 open reading frame 78
## 48757                                                                                                 transcriptional adaptor 2A
## 48761                                                                                            dual specificity phosphatase 14
## 48763                                                                                                             synergin gamma
## 48765                                                                                                       DExD-box helicase 52
## 48770                                                                                                            HNF1 homeobox B
## 48776                                                                                               TBC1 domain family member 3F
## 48779                                                                                                TBC1 domain family member 3
## 48780                                                                                                TBC1 domain family member 3
## 48783                                                                                        mitochondrial ribosomal protein L45
## 48785                                                                                             G protein-coupled receptor 179
## 48787                                                                                         suppressor of cytokine signaling 7
## 48790                                                                                           Rho GTPase activating protein 23
## 48793                                                                                           SRC kinase signaling inhibitor 1
## 48801                                                                                               MLLT6, PHD finger containing
## 48806                                                                                                 CDGSH iron sulfur domain 3
## 48809                                                                                               polycomb group ring finger 2
## 48812                                                                                              proteasome 20S subunit beta 3
## 48815                                                                      phosphatidylinositol-5-phosphate 4-kinase type 2 beta
## 48817                                                                               CWC25 spliceosome associated protein homolog
## 48820                                                                                        chromosome 17 open reading frame 98
## 48914                                                                                                                 keratin 12
## 48916                                                                                                                 keratin 20
## 48919                                                                                                                 keratin 23
## 48921                                                                                                                 keratin 39
## 48923                                                                                                                 keratin 40
## 48925                                                                                             keratin associated protein 3-3
## 48927                                                                                             keratin associated protein 3-2
## 48930                                                                                             keratin associated protein 3-1
## 48932                                                                                             keratin associated protein 1-5
## 48934                                                                                             keratin associated protein 1-4
## 48936                                                                                             keratin associated protein 1-3
## 48938                                                                                             keratin associated protein 1-1
## 48940                                                                                             keratin associated protein 2-1
## 48942                                                                                             keratin associated protein 2-2
## 48944                                                                                             keratin associated protein 2-3
## 48946                                                                                             keratin associated protein 2-4
## 48950                                                                                             keratin associated protein 4-8
## 48953                                                                                             keratin associated protein 4-9
## 48955                                                                                            keratin associated protein 4-11
## 48957                                                                                            keratin associated protein 4-12
## 48968                                                                                             keratin associated protein 9-2
## 48969                                                                                             keratin associated protein 9-2
## 48971                                                                                             keratin associated protein 9-3
## 48974                                                                                             keratin associated protein 9-4
## 48975                                                                                             keratin associated protein 9-4
## 48977                                                                                             keratin associated protein 9-9
## 48978                                                                                             keratin associated protein 9-9
## 48980                                                                                             keratin associated protein 9-6
## 48981                                                                                             keratin associated protein 9-6
## 48984                                                                                             keratin associated protein 9-7
## 48987                                                                                       keratin associated like protein 29-1
## 48988                                                                                       keratin associated like protein 29-1
## 48990                                                                                            keratin associated protein 16-1
## 48992                                                                                            keratin associated protein 17-1
## 48996                                                                                                                keratin 33A
## 48998                                                                                                                keratin 33B
## 49000                                                                                                                 keratin 34
## 49002                                                                                                                 keratin 31
## 49006                                                                                                                 keratin 37
## 49223                                                                          mitogen-activated protein kinase kinase kinase 14
## 49227                                                                                           Rho GTPase activating protein 27
## 49228                                                                                           Rho GTPase activating protein 27
## 49232                                                                           pleckstrin homology and RUN domain containing M1
## 49233                                                                           pleckstrin homology and RUN domain containing M1
## 49248                                                                                 corticotropin releasing hormone receptor 1
## 49249                                                                                 corticotropin releasing hormone receptor 1
## 49250                                                                                 corticotropin releasing hormone receptor 1
## 49251                                                                                 corticotropin releasing hormone receptor 1
## 49257                                                                                           signal peptide peptidase like 2C
## 49258                                                                                           signal peptide peptidase like 2C
## 49260                                                                                         microtubule associated protein tau
## 49261                                                                                         microtubule associated protein tau
## 49264                                                                                                                   saitohin
## 49266                                                                                      KAT8 regulatory NSL complex subunit 1
## 49267                                                                                      KAT8 regulatory NSL complex subunit 1
## 49271                                                                                                     KANSL1 antisense RNA 1
## 49272                                                                                                     KANSL1 antisense RNA 1
## 49277                                                                                    ADP ribosylation factor like GTPase 17B
## 49278                                                                                    ADP ribosylation factor like GTPase 17B
## 49280                                                                                         leucine rich repeat containing 37A
## 49285                                                                                leucine rich repeat containing 37 member A2
## 49286                                                                                leucine rich repeat containing 37 member A2
## 49288                                                                                    ADP ribosylation factor like GTPase 17A
## 49289                                                                                    ADP ribosylation factor like GTPase 17A
## 49290                                                                                    ADP ribosylation factor like GTPase 17A
## 49294                                                                   N-ethylmaleimide sensitive factor, vesicle fusing ATPase
## 49295                                                                   N-ethylmaleimide sensitive factor, vesicle fusing ATPase
## 49298                                                                                                        Wnt family member 3
## 49299                                                                                                        Wnt family member 3
## 49301                                                                                                       Wnt family member 9B
## 49598                                                                                                     ring finger protein 43
## 49805                                                                                leucine rich repeat containing 37 member A3
## 49937                                                                                         solute carrier family 39 member 11
## 50265                                                                                                          glucagon receptor
## 50269                                                                                protein phosphatase 1 regulatory subunit 27
## 50337                                                                                                 tubulin folding cofactor D
## 50344                                                         UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase like 1
## 50347                                                                        meteorin like, glial cell differentiation regulator
## 50741                                                                             cutaneous T cell lymphoma-associated antigen 1
## 51019                                                                cap binding complex dependent translation initiation factor
## 51021                                                                                                              microRNA 4743
## 51060                                                                       spindle and kinetochore associated complex subunit 1
## 51064                                                                                         mitogen-activated protein kinase 4
## 51281                                                                                            dermatan sulfate epimerase like
## 51409                                                                                          spalt like transcription factor 3
## 51410                                                                                          spalt like transcription factor 3
## 51412                                                                             ATPase phospholipid transporting 9B (putative)
## 51413                                                                             ATPase phospholipid transporting 9B (putative)
## 51423                                                                                                  CTD phosphatase subunit 1
## 51649                                                                                         MKKS centrosomal shuttling protein
## 51650                                                                                         MKKS centrosomal shuttling protein
## 51981                                                                                                   COMM domain containing 7
## 52222                                                                             L3MBTL histone methyl-lysine binding protein 1
## 52596                                                                                                                 cadherin 4
## 52600                                                                               TATA-box binding protein associated factor 4
## 52667                                                                       potassium voltage-gated channel subfamily Q member 2
## 52713                                                                                       opioid related nociceptin receptor 1
## 52716                                                                                           neuropeptides B and W receptor 2
## 52718                                                                                              myelin transcription factor 1
## 52720                                               protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 2
## 52781                                                                                                               azurocidin 1
## 52783                                                                                                               proteinase 3
## 52785                                                                                             elastase, neutrophil expressed
## 52787                                                                                                        complement factor D
## 52789                                                                                                mediator complex subunit 16
## 52808                                                                                                 strawberry notch homolog 2
## 53217                                                                                                    zinc finger protein 177
## 53367                                                                                                    zinc finger protein 844
## 53467                                                                                         zinc finger SWIM-type containing 4
## 53471                                                                                                              microRNA 24-2
## 53473                                                                                                               microRNA 27a
## 53475                                                                                                               microRNA 23a
## 53477                                                                                              nanos C2HC-type zinc finger 3
## 53479                                                                                                              microRNA 181c
## 53481                                                                                                              microRNA 181d
## 53484                                                                                    coiled-coil and C2 domain containing 1A
## 53486                                                                                                             podocan like 1
## 53488                                                                                         DDB1 and CUL4 associated factor 15
## 53490                                                                                                       regulatory factor X1
## 53492                                                                                                                  relaxin 3
## 53495                                                                                      interleukin 27 receptor subunit alpha
## 53497                                                                                                               paralemmin 3
## 53501                                                                                        chromosome 19 open reading frame 67
## 53503                                                                                    sterile alpha motif domain containing 1
## 53505                                                                      protein kinase cAMP-activated catalytic subunit alpha
## 53508                                                                               anti-silencing function 1B histone chaperone
## 53716                                                                                                       phosphodiesterase 4C
## 53845                                                                                                     zinc finger protein 66
## 53850                                                                                                     zinc finger protein 85
## 53855                                                                                                    zinc finger protein 430
## 53892                                                                                                    zinc finger protein 100
## 53898                                                                                                     zinc finger protein 43
## 53913                                                                                                    zinc finger protein 676
## 53918                                                                                                    zinc finger protein 729
## 54132                                                                                LSM14A mRNA processing body assembly factor
## 54137                                                                                              glucose-6-phosphate isomerase
## 54362                                                                    mitogen-activated protein kinase kinase kinase kinase 1
## 54365                                                                       eukaryotic translation initiation factor 3 subunit K
## 54367                                                                                                            actinin alpha 4
## 54372                                                                                                                 galectin 7
## 54373                                                                                                                 galectin 7
## 54374                                                                                                                 galectin 7
## 54376                                                                                                                galectin 7B
## 54377                                                                                                                galectin 7B
## 54378                                                                                                                galectin 7B
## 54381                                                                                                                 galectin 4
## 54383                                                                                                      enoyl-CoA hydratase 1
## 54387                                                                                  heterogeneous nuclear ribonucleoprotein L
## 54390                                                                                                Ras and Rab interactor like
## 54393                                                                                                                  sirtuin 2
## 54395                                                                                                        NFKB inhibitor beta
## 54398                                                                                     seryl-tRNA synthetase 2, mitochondrial
## 54401                                                                                        mitochondrial ribosomal protein S12
## 54404                                                                                                           F-box protein 17
## 54458                                                                                                    leucine twenty homeobox
## 54460                                                              dual specificity tyrosine phosphorylation regulated kinase 1B
## 54462                                                                                                                fibrillarin
## 54464                                                                                                   Fc gamma binding protein
## 54467                                                                                           proteasome 26S subunit, ATPase 4
## 54469                                                                                                    zinc finger protein 546
## 54474                                                                                                   zinc finger protein 780B
## 54477                                                                                                   zinc finger protein 780A
## 54554                                                                                              CEA cell adhesion molecule 21
## 54558                                                                                               CEA cell adhesion molecule 4
## 54563                                                                                               CEA cell adhesion molecule 7
## 55311                                                                                V-set and transmembrane domain containing 1
## 55312                                                                                V-set and transmembrane domain containing 1
## 55313                                                                                V-set and transmembrane domain containing 1
## 55314                                                                                V-set and transmembrane domain containing 1
## 55315                                                                                V-set and transmembrane domain containing 1
## 55316                                                                                V-set and transmembrane domain containing 1
## 55317                                                                                V-set and transmembrane domain containing 1
## 55318                                                                                V-set and transmembrane domain containing 1
## 55319                                                                                V-set and transmembrane domain containing 1
## 55321                                                                 T cell-interacting, activating receptor on myeloid cells 1
## 55322                                                                 T cell-interacting, activating receptor on myeloid cells 1
## 55323                                                                 T cell-interacting, activating receptor on myeloid cells 1
## 55324                                                                 T cell-interacting, activating receptor on myeloid cells 1
## 55325                                                                 T cell-interacting, activating receptor on myeloid cells 1
## 55326                                                                 T cell-interacting, activating receptor on myeloid cells 1
## 55327                                                                 T cell-interacting, activating receptor on myeloid cells 1
## 55328                                                                 T cell-interacting, activating receptor on myeloid cells 1
## 55329                                                                 T cell-interacting, activating receptor on myeloid cells 1
## 55331                                                                                     osteoclast associated Ig-like receptor
## 55332                                                                                     osteoclast associated Ig-like receptor
## 55333                                                                                     osteoclast associated Ig-like receptor
## 55334                                                                                     osteoclast associated Ig-like receptor
## 55335                                                                                     osteoclast associated Ig-like receptor
## 55336                                                                                     osteoclast associated Ig-like receptor
## 55337                                                                                     osteoclast associated Ig-like receptor
## 55338                                                                                     osteoclast associated Ig-like receptor
## 55339                                                                                     osteoclast associated Ig-like receptor
## 55341                                                                                  NADH:ubiquinone oxidoreductase subunit A3
## 55342                                                                                  NADH:ubiquinone oxidoreductase subunit A3
## 55343                                                                                  NADH:ubiquinone oxidoreductase subunit A3
## 55344                                                                                  NADH:ubiquinone oxidoreductase subunit A3
## 55345                                                                                  NADH:ubiquinone oxidoreductase subunit A3
## 55346                                                                                  NADH:ubiquinone oxidoreductase subunit A3
## 55347                                                                                  NADH:ubiquinone oxidoreductase subunit A3
## 55348                                                                                  NADH:ubiquinone oxidoreductase subunit A3
## 55349                                                                                  NADH:ubiquinone oxidoreductase subunit A3
## 55351                                                                                                        TCF3 fusion partner
## 55352                                                                                                        TCF3 fusion partner
## 55353                                                                                                        TCF3 fusion partner
## 55354                                                                                                        TCF3 fusion partner
## 55355                                                                                                        TCF3 fusion partner
## 55356                                                                                                        TCF3 fusion partner
## 55357                                                                                                        TCF3 fusion partner
## 55358                                                                                                        TCF3 fusion partner
## 55359                                                                                                        TCF3 fusion partner
## 55361                                                                                              pre-mRNA processing factor 31
## 55362                                                                                              pre-mRNA processing factor 31
## 55363                                                                                              pre-mRNA processing factor 31
## 55364                                                                                              pre-mRNA processing factor 31
## 55365                                                                                              pre-mRNA processing factor 31
## 55366                                                                                              pre-mRNA processing factor 31
## 55367                                                                                              pre-mRNA processing factor 31
## 55368                                                                                              pre-mRNA processing factor 31
## 55369                                                                                              pre-mRNA processing factor 31
## 55372                                                                                   CCR4-NOT transcription complex subunit 3
## 55373                                                                                   CCR4-NOT transcription complex subunit 3
## 55374                                                                                   CCR4-NOT transcription complex subunit 3
## 55375                                                                                   CCR4-NOT transcription complex subunit 3
## 55376                                                                                   CCR4-NOT transcription complex subunit 3
## 55377                                                                                   CCR4-NOT transcription complex subunit 3
## 55378                                                                                   CCR4-NOT transcription complex subunit 3
## 55379                                                                                   CCR4-NOT transcription complex subunit 3
## 55380                                                                                   CCR4-NOT transcription complex subunit 3
## 55382                                                                                        leukocyte receptor cluster member 1
## 55383                                                                                        leukocyte receptor cluster member 1
## 55384                                                                                        leukocyte receptor cluster member 1
## 55385                                                                                        leukocyte receptor cluster member 1
## 55386                                                                                        leukocyte receptor cluster member 1
## 55387                                                                                        leukocyte receptor cluster member 1
## 55388                                                                                        leukocyte receptor cluster member 1
## 55389                                                                                        leukocyte receptor cluster member 1
## 55390                                                                                        leukocyte receptor cluster member 1
## 55392                                                                                               transmembrane channel like 4
## 55393                                                                                               transmembrane channel like 4
## 55394                                                                                               transmembrane channel like 4
## 55395                                                                                               transmembrane channel like 4
## 55396                                                                                               transmembrane channel like 4
## 55397                                                                                               transmembrane channel like 4
## 55398                                                                                               transmembrane channel like 4
## 55399                                                                                               transmembrane channel like 4
## 55400                                                                                               transmembrane channel like 4
## 55402                                                                       membrane bound O-acyltransferase domain containing 7
## 55403                                                                       membrane bound O-acyltransferase domain containing 7
## 55404                                                                       membrane bound O-acyltransferase domain containing 7
## 55405                                                                       membrane bound O-acyltransferase domain containing 7
## 55406                                                                       membrane bound O-acyltransferase domain containing 7
## 55407                                                                       membrane bound O-acyltransferase domain containing 7
## 55408                                                                       membrane bound O-acyltransferase domain containing 7
## 55409                                                                       membrane bound O-acyltransferase domain containing 7
## 55410                                                                       membrane bound O-acyltransferase domain containing 7
## 55412                                                                                      tRNA splicing endonuclease subunit 34
## 55413                                                                                      tRNA splicing endonuclease subunit 34
## 55414                                                                                      tRNA splicing endonuclease subunit 34
## 55415                                                                                      tRNA splicing endonuclease subunit 34
## 55416                                                                                      tRNA splicing endonuclease subunit 34
## 55417                                                                                      tRNA splicing endonuclease subunit 34
## 55418                                                                                      tRNA splicing endonuclease subunit 34
## 55419                                                                                      tRNA splicing endonuclease subunit 34
## 55420                                                                                      tRNA splicing endonuclease subunit 34
## 55424                                                                                                       ribosomal protein S9
## 55425                                                                                                       ribosomal protein S9
## 55426                                                                                                       ribosomal protein S9
## 55427                                                                                                       ribosomal protein S9
## 55428                                                                                                       ribosomal protein S9
## 55429                                                                                                       ribosomal protein S9
## 55430                                                                                                       ribosomal protein S9
## 55431                                                                                                       ribosomal protein S9
## 55432                                                                                                       ribosomal protein S9
## 55435                                                                                  leukocyte immunoglobulin like receptor B3
## 55436                                                                                  leukocyte immunoglobulin like receptor B3
## 55437                                                                                  leukocyte immunoglobulin like receptor B3
## 55439                                                                                  leukocyte immunoglobulin like receptor A6
## 55440                                                                                  leukocyte immunoglobulin like receptor A6
## 55441                                                                                  leukocyte immunoglobulin like receptor A6
## 55442                                                                                  leukocyte immunoglobulin like receptor A6
## 55448                                                                                  leukocyte immunoglobulin like receptor B5
## 55449                                                                                  leukocyte immunoglobulin like receptor B5
## 55450                                                                                  leukocyte immunoglobulin like receptor B5
## 55451                                                                                  leukocyte immunoglobulin like receptor B5
## 55456                                                                                  leukocyte immunoglobulin like receptor B2
## 55457                                                                                  leukocyte immunoglobulin like receptor B2
## 55458                                                                                  leukocyte immunoglobulin like receptor B2
## 55459                                                                                  leukocyte immunoglobulin like receptor B2
## 55463                                                                                  leukocyte immunoglobulin like receptor A3
## 55464                                                                                  leukocyte immunoglobulin like receptor A3
## 55465                                                                                  leukocyte immunoglobulin like receptor A3
## 55469                                                                                  leukocyte immunoglobulin like receptor A5
## 55470                                                                                  leukocyte immunoglobulin like receptor A5
## 55471                                                                                  leukocyte immunoglobulin like receptor A5
## 55472                                                                                  leukocyte immunoglobulin like receptor A5
## 55477                                                                                  leukocyte immunoglobulin like receptor A4
## 55478                                                                                  leukocyte immunoglobulin like receptor A4
## 55479                                                                                  leukocyte immunoglobulin like receptor A4
## 55482                                                                        leukocyte associated immunoglobulin like receptor 1
## 55483                                                                        leukocyte associated immunoglobulin like receptor 1
## 55484                                                                        leukocyte associated immunoglobulin like receptor 1
## 55485                                                                        leukocyte associated immunoglobulin like receptor 1
## 55488                                                                                                     tweety family member 1
## 55489                                                                                                     tweety family member 1
## 55490                                                                                                     tweety family member 1
## 55496                                                                                                      LENG8 antisense RNA 1
## 55499                                                                                        leukocyte receptor cluster member 8
## 55500                                                                                        leukocyte receptor cluster member 8
## 55501                                                                                        leukocyte receptor cluster member 8
## 55503                                                                                        leukocyte receptor cluster member 9
## 55504                                                                                        leukocyte receptor cluster member 9
## 55505                                                                                        leukocyte receptor cluster member 9
## 55507                                                                                                   CDC42 effector protein 5
## 55508                                                                                                   CDC42 effector protein 5
## 55509                                                                                                   CDC42 effector protein 5
## 55511                                                                        leukocyte associated immunoglobulin like receptor 2
## 55512                                                                        leukocyte associated immunoglobulin like receptor 2
## 55513                                                                        leukocyte associated immunoglobulin like receptor 2
## 55518                                                                                  leukocyte immunoglobulin like receptor A2
## 55519                                                                                  leukocyte immunoglobulin like receptor A2
## 55520                                                                                  leukocyte immunoglobulin like receptor A2
## 55522                                                                                  leukocyte immunoglobulin like receptor B1
## 55523                                                                                  leukocyte immunoglobulin like receptor B1
## 55524                                                                                  leukocyte immunoglobulin like receptor B1
## 55525                                                                                  leukocyte immunoglobulin like receptor B1
## 55528                                                                                  leukocyte immunoglobulin like receptor A1
## 55529                                                                                  leukocyte immunoglobulin like receptor A1
## 55530                                                                                  leukocyte immunoglobulin like receptor A1
## 55535                                                                                  leukocyte immunoglobulin like receptor B4
## 55536                                                                                  leukocyte immunoglobulin like receptor B4
## 55537                                                                                  leukocyte immunoglobulin like receptor B4
## 55538                                                                                  leukocyte immunoglobulin like receptor B4
## 55546                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55547                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55548                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55549                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55550                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55551                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55552                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55553                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55554                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55555                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55556                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55557                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55558                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55559                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55560                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55561                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55562                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55563                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55564                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55565                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55566                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55567                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55568                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55569                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55570                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55571                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55572                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55573                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55574                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55575                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55576                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55577                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55578                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55579                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55580                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55581                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55582                                                                        leukocyte immunoglobulin-like receptor pseudogene 2
## 55584                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55585                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55586                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55587                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55588                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55589                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55590                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55591                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55592                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55593                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55594                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55595                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55596                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55597                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55598                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55599                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55600                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55601                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55602                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55603                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55604                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55605                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55606                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55607                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55608                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55609                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55610                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55611                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55612                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55613                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55614                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1
## 55616                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55617                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55618                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55619                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55620                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55621                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55622                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55623                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55624                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55625                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55626                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55627                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55628                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55629                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55630                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55631                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55632                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55633                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55634                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55635                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55636                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55637                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55638                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55639                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55640                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55641                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55642                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55643                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55644                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55645                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55646                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55647                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55648                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55649                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55650                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55651                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55652                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55653                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55654                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55655                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55656                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3
## 55659                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55660                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55661                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55662                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55663                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55664                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55665                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55666                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55667                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55668                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55669                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55670                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55671                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55672                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55673                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55674                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55675                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55676                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55677                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55678                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55679                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55680                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55681                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55682                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55683                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55684                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55685                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55686                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55687                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55688                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55689                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55690                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55691                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55692                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55693                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55694                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55695                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55696                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55697                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55698                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4
## 55700                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55701                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55702                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55703                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55704                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55705                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55706                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55707                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55708                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55709                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55710                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55711                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55712                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55713                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55714                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55715                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55716                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55717                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55718                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55719                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55720                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55721                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55722                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55723                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55724                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55725                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55726                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55727                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55728                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55729                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3
## 55732                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55733                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55734                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55735                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55736                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55737                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55738                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55739                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55740                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55741                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55742                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55743                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55744                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55745                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55746                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55747                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55748                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55749                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55750                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55751                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55752                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55753                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55754                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55755                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55756                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55757                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55758                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55759                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55760                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55761                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55762                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55763                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55764                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1
## 55767                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55768                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55769                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55770                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55771                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55772                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55773                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55774                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55775                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55776                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55777                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55778                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55779                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55780                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55781                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55782                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55783                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55784                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55785                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55786                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55787                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55788                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55789                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55790                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55791                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55792                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55793                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55794                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55795                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55796                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55797                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55798                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4
## 55800                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55801                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55802                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55803                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55804                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55805                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55806                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55807                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55808                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55809                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55810                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55811                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55812                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55813                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55814                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55815                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55816                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55817                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55818                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55819                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55820                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55821                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55822                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55823                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55824                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55825                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55826                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55827                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55828                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55829                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55830                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55831                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55832                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55833                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55834                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55835                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55836                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55837                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55838                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55839                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55840                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55841                                     killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2
## 55844                                                                                                          Fc alpha receptor
## 55845                                                                                                          Fc alpha receptor
## 55846                                                                                                          Fc alpha receptor
## 55847                                                                                                          Fc alpha receptor
## 55848                                                                                                          Fc alpha receptor
## 55849                                                                                                          Fc alpha receptor
## 55850                                                                                                          Fc alpha receptor
## 55851                                                                                                          Fc alpha receptor
## 55852                                                                                                          Fc alpha receptor
## 55853                                                                                                          Fc alpha receptor
## 55854                                                                                                          Fc alpha receptor
## 55855                                                                                                          Fc alpha receptor
## 55856                                                                                                          Fc alpha receptor
## 55857                                                                                                          Fc alpha receptor
## 55860                                                                                 natural cytotoxicity triggering receptor 1
## 55861                                                                                 natural cytotoxicity triggering receptor 1
## 55862                                                                                 natural cytotoxicity triggering receptor 1
## 55863                                                                                 natural cytotoxicity triggering receptor 1
## 55864                                                                                 natural cytotoxicity triggering receptor 1
## 55865                                                                                 natural cytotoxicity triggering receptor 1
## 55866                                                                                 natural cytotoxicity triggering receptor 1
## 55867                                                                                 natural cytotoxicity triggering receptor 1
## 55868                                                                                 natural cytotoxicity triggering receptor 1
## 55869                                                                                 natural cytotoxicity triggering receptor 1
## 55870                                                                                 natural cytotoxicity triggering receptor 1
## 55871                                                                                 natural cytotoxicity triggering receptor 1
## 55872                                                                                 natural cytotoxicity triggering receptor 1
## 55873                                                                                 natural cytotoxicity triggering receptor 1
## 55874                                                                                 natural cytotoxicity triggering receptor 1
## 55875                                                                                 natural cytotoxicity triggering receptor 1
## 55876                                                                                 natural cytotoxicity triggering receptor 1
## 55878                                                                                       NLR family pyrin domain containing 7
## 55879                                                                                       NLR family pyrin domain containing 7
## 55880                                                                                       NLR family pyrin domain containing 7
## 55881                                                                                       NLR family pyrin domain containing 7
## 55882                                                                                       NLR family pyrin domain containing 7
## 55883                                                                                       NLR family pyrin domain containing 7
## 55884                                                                                       NLR family pyrin domain containing 7
## 55885                                                                                       NLR family pyrin domain containing 7
## 55886                                                                                       NLR family pyrin domain containing 7
## 55889                                                                                       NLR family pyrin domain containing 2
## 55890                                                                                       NLR family pyrin domain containing 2
## 55891                                                                                       NLR family pyrin domain containing 2
## 55892                                                                                       NLR family pyrin domain containing 2
## 55893                                                                                       NLR family pyrin domain containing 2
## 55894                                                                                       NLR family pyrin domain containing 2
## 55895                                                                                       NLR family pyrin domain containing 2
## 55896                                                                                       NLR family pyrin domain containing 2
## 55897                                                                                       NLR family pyrin domain containing 2
## 55901                                                                                                   glycoprotein VI platelet
## 55902                                                                                                   glycoprotein VI platelet
## 55903                                                                                                   glycoprotein VI platelet
## 55904                                                                                                   glycoprotein VI platelet
## 55905                                                                                                   glycoprotein VI platelet
## 55906                                                                                                   glycoprotein VI platelet
## 55907                                                                                                   glycoprotein VI platelet
## 55908                                                                                                   glycoprotein VI platelet
## 55909                                                                                                   glycoprotein VI platelet
## 55912                                                                                                   retinol dehydrogenase 13
## 55913                                                                                                   retinol dehydrogenase 13
## 55914                                                                                                   retinol dehydrogenase 13
## 55915                                                                                                   retinol dehydrogenase 13
## 55916                                                                                                   retinol dehydrogenase 13
## 55917                                                                                                   retinol dehydrogenase 13
## 55918                                                                                                   retinol dehydrogenase 13
## 55919                                                                                                   retinol dehydrogenase 13
## 55920                                                                                                   retinol dehydrogenase 13
## 56125                                                                                                    zinc finger protein 544
## 56487                                                                                    testis-specific transcript, Y-linked 13
## 56605                                                                                   testis-specific transcript, Y-linked 17C
## 57009                                                                                                   zinc finger protein 280B
## 57011                                                                                                   zinc finger protein 280A
## 57013                                                                           PRAME nuclear receptor transcriptional regulator
## 57015                                                                                                  uncharacterized LOC648691
## 57117                                                                                        chromosome 22 open reading frame 15
## 57119                                                                   coiled-coil-helix-coiled-coil-helix domain containing 10
## 57121                                                                                                 matrix metallopeptidase 11
## 57124                          SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1
## 57126                                                                                                                   derlin 3
## 57129                                                                                          solute carrier family 2 member 11
## 57133                                                                                     macrophage migration inhibitory factor
## 57140                                                                                         glutathione S-transferase theta 2B
## 57143                                                                                              D-dopachrome tautomerase like
## 57144                                                                                              D-dopachrome tautomerase like
## 57145                                                                                              D-dopachrome tautomerase like
## 57148                                                                                                   D-dopachrome tautomerase
## 57149                                                                                                   D-dopachrome tautomerase
## 57152                                                                        glutathione S-transferase theta 2 (gene/pseudogene)
## 57165                                                                                              calcineurin binding protein 1
## 57182                                                                                                gamma-glutamyltransferase 1
## 57469                                                                                                          apolipoprotein L5
## 57471                                                                                                RNA binding fox-1 homolog 2
## 57499                                                                                                                parvalbumin
## 57503                                                                                              neutrophil cytosolic factor 4
## 57526                                             extracellular leucine rich repeat and fibronectin type III domain containing 2
## 57600                                                                  apolipoprotein B mRNA editing enzyme catalytic subunit 3A
## 57603                                                                                                   APOBEC3B antisense RNA 1
## 57625                                                                                          mitochondrial elongation factor 1
## 57710                                                                    single-pass membrane protein with aspartate rich tail 1
## 57711                                                                    single-pass membrane protein with aspartate rich tail 1
## 57712                                                                    single-pass membrane protein with aspartate rich tail 1
## 57714                                                                                  NADH:ubiquinone oxidoreductase subunit A6
## 57715                                                                                  NADH:ubiquinone oxidoreductase subunit A6
## 57716                                                                                  NADH:ubiquinone oxidoreductase subunit A6
## 57717                                                                                  NADH:ubiquinone oxidoreductase subunit A6
## 57722                                                                              cytochrome P450 family 2 subfamily D member 6
## 57723                                                                              cytochrome P450 family 2 subfamily D member 6
## 57724                                                                              cytochrome P450 family 2 subfamily D member 6
## 57725                                                                              cytochrome P450 family 2 subfamily D member 6
## 57726                                                                              cytochrome P450 family 2 subfamily D member 6
## 57732                                                                                                    transcription factor 20
## 57733                                                                                                    transcription factor 20
## 57734                                                                                                    transcription factor 20
## 57735                                                                                                    transcription factor 20
## 57736                                                                                                    transcription factor 20
## 57737                                                                                                    transcription factor 20
## 57738                                                                                                    transcription factor 20
## 57932                                                                                                                    acrosin
## 58045                                                                                            BTG anti-proliferation factor 3
## 58093                                                                                 long intergenic non-protein coding RNA 308
## 58280                                                                                            PAX3 and PAX7 binding protein 1
## 58283                                                                                        chromosome 21 open reading frame 62
## 58295                                                                               interferon alpha and beta receptor subunit 2
## 58303                                                                                                interferon gamma receptor 2
## 58305                                                                                                  transmembrane protein 50B
## 58310                                                                          DnaJ heat shock protein family (Hsp40) member C28
## 58312 phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase
## 58632                                                                                      formimidoyltransferase cyclodeaminase
## 58634                                                                                                       FTCD antisense RNA 1
## 58636                                                                            spermatogenesis and centriole associated 1 like
## 58639                                                                                                        lanosterol synthase
## 58747                                                                      major histocompatibility complex, class II, DR beta 4
## 58748                                                                      major histocompatibility complex, class II, DR beta 4
## 58987                                                                      major histocompatibility complex, class II, DR beta 3
## 58988                                                                      major histocompatibility complex, class II, DR beta 3
## 59183                                                                                                          serine protease 2
## 59188                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 2
## 59189                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 2
## 59190                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 2
## 59191                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 2
## 59192                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 2
## 59193                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 2
## 59194                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 2
## 59195                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 2
## 59196                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 2
## 59197                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 2
## 59198                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 2
## 59199                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 2
## 59235                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 1
## 59236                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 1
## 59237                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 1
## 59238                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 1
## 59239                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 1
## 59240                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 1
## 59241                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 1
## 59242                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 1
## 59243                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 1
## 59244                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 1
## 59245                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 1
## 59247                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 2
## 59248                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 2
## 59249                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 2
## 59250                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 2
## 59251                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 2
## 59252                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 2
## 59253                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 2
## 59254                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 2
## 59255                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 2
## 59256                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 2
## 59257                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 2
## 59258                                       killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 2
## 59262                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 5
## 59263                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 5
## 59264                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 5
## 59265                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 5
## 59266                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 5
## 59267                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 5
## 59268                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 5
## 59269                                      killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 5

⊕Tip: Alternatively, you could perform the edgeR filtering function, filterByExpr, prior to running these annotations. There’s two approaches to handle these genes as discussed by Law et al. (2018b):

• We could combine and merge all information from the multi-mapped genes such that the IDs and gene names would be merged into one column (i.e. SYMBOL TBCE would have an ENSEMBL id of ENSG00000282984 and ENSG00000285053).
  • This is not recommended as merging the expression values for gene IDs requires proper rationale.
• We select one of the entries to represent the gene with duplicated annotations.⊕
  NOTE: This duplicate removal by gene symbol ID only keeps the first occurrence. This will remove the following non-specific ENSEMBL, ENTREZID, or GENENAME entries. One solution is to perform gene set testing separately from gene annotations (not covered in this pipeline).
  • This is recommended as later on, we will filter out most unexpressed or very low expressed genes. In addition, depending on the enrichment used, the noise of the expression measurements is tolerable (i.e. ncRNAs were not selected for in the enrichment).

For simplicity purposes, we perform the second solution.

To achieve 1:1 mapping for our DGEList counts, we can remove the duplicates using the following code:

#Remove duplicates using the gene symbols
annot.gene.ids <- annot.gene.ids %>% 
  .[!duplicated(.$SYMBOL), ]

We can also add the gene lengths from the featureCounts protocol to the annot.gene.ids using the original seqdata raw counts table.

#Merge a new gene lengths column at the end of the annot.gene.ids 
#using the columns where the SYMBOL values are the same 
# Note: The column names are referenced directly in quotes
  annot.gene.ids <- annot.gene.ids %>% 
    left_join(., seqdata[, c("Geneid", "Length")], by = c('SYMBOL' = 'Geneid'))

Let’s take a look at our gene annotations.

#View the gene annotations 
annot.gene.ids

Let’s also confirm the SYMBOL column entries matches exactly to the row names of split.DGElist[["komenredo.counts"]][["counts"]].

all(annot.gene.ids$SYMBOL == rownames(split.DGElist[["komenredo.counts"]][["counts"]]))

## [1] TRUE

Now that we have 1:1 matches with gene symbols and their corresponding annotations, we can append this to the DGEList $genes slot. ⊕Tip: Since all the experiments came from the same seqdata counts dataset, you could use this annotation information for the other experiments that focus on the human reference genome as well. Like with the sample annotations, the annot.gene.ids data frame is neatly stored and associated with the DGEList and the raw counts data.

split.DGElist[["komenredo.counts"]]$genes <- annot.gene.ids

# Annotated DGEList object with sample and gene information
split.DGElist[["komenredo.counts"]]

## An object of class "DGEList"
## $counts
##            TTCCATTC.ATGTATCA TACAGAGT.ATGTATCA TCAAGGAT.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                   154               225               578
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CCACAATG.TCATATAT CTGGTCGT.TCATATAT ACACAACA.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   248               268               145
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CGCGTGAT.ATGTATCA TCCTATCT.TCATATAT AACCAATC.TCATATAT
## DDX11L1                    8                 0                 0
## WASH7P                   246               212               111
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            TCTATTGG.TCATATAT TTCACACT.ATGTATCA CGCTCTTG.ATGTATCA
## DDX11L1                    0                 0                 2
## WASH7P                   140               115               229
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            ACTCACCG.ATGTATCA TGGTACAG.TCATATAT CCTGTTAC.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   283               285               221
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CGCAACAG.ATGTATCA CTAGCCGA.ATGTATCA ACTCGAAT.ATGTATCA
## DDX11L1                    1                 0                 0
## WASH7P                   157               136               155
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            GATGAGAA.ATGTATCA CCTACACA.ATGTATCA ACCTGAGC.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                   250               143               145
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            AACGCTTG.TCATATAT CATCTTCT.ATGTATCA ATTCGCAG.TCATATAT
## DDX11L1                    0                 6                 0
## WASH7P                   262               278               159
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            GGTGTGAC.TCATATAT CGTAATTC.TCATATAT ACATCCTT.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   247               241               116
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CGATGGCA.ATGTATCA CCAGGTAA.ATGTATCA GTTAAGCA.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   190                98               148
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CTGTACGC.TCATATAT CTAACAAC.ATGTATCA TCAACTGA.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   174               204               165
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            GTTCGTCT.TCATATAT CCTTATGT.TCATATAT ATTCCGTA.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                   142               169                90
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CCGAGTTA.TCATATAT CTCGTACA.ATGTATCA TCCTCAGA.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                    92               239               143
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CGAGCATT.TCATATAT TGAATGTG.TCATATAT GGCTCCTA.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   345               117               100
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            TCAGATAC.TCATATAT CCATACTC.ATGTATCA TGAATGTG.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   183               158               149
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            AATGTGCC.ATGTATCA TGTAAGAC.TCATATAT GGAGCTAT.TCATATAT
## DDX11L1                    0                 0                 1
## WASH7P                   166                74                62
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CGCTCTTG.TCATATAT TGAACTCT.ATGTATCA AACGCTTG.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   261               230               292
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            ATGACACC.ATGTATCA TCACTCAC.ATGTATCA ATGGAACA.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   131               183                83
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            GTGCGAGT.ATGTATCA TGTTGCAC.ATGTATCA ACCGTTCC.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                   164               119               144
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CACATGGT.TCATATAT ATGGTCCG.ATGTATCA CTTGTTGG.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   306               105               352
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            ACGAAGCG.TCATATAT CCATTGCG.TCATATAT ATAGATCC.ATGTATCA
## DDX11L1                    0                 0                 8
## WASH7P                   235               237               186
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            ATTCCGTA.ATGTATCA CAGGCCAT.ATGTATCA CAGGCTTC.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                    85               139               232
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            TACAGAGT.TCATATAT ATGGTCCG.TCATATAT TTGGCTGC.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                   113               179               104
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CACAGTCT.ATGTATCA ACGCTGCA.ATGTATCA CGTAATTC.ATGTATCA
## DDX11L1                    2                 0                 0
## WASH7P                   132               182               174
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            TCTATTGG.ATGTATCA ACTCACCG.TCATATAT TCCTTGGC.ATGTATCA
## DDX11L1                    0                 2                 6
## WASH7P                    71                72               203
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            ACGAAGCG.ATGTATCA ATGCCGCT.ATGTATCA CAGAGTGG.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                   310               236                60
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CTGTACGC.ATGTATCA GTTCGTCT.ATGTATCA TTCACACT.TCATATAT
## DDX11L1                    2                 0                 0
## WASH7P                    90               135               226
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CAGGAAGG.ATGTATCA GTTAAGCA.TCATATAT GGCTCCTA.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                   209               168               141
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CTCGTACA.TCATATAT GGAGCTAT.ATGTATCA CGACTAGC.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   180                77               257
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            TCCTATCT.ATGTATCA TGGTACAG.ATGTATCA GTTGACAG.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   326               230               219
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CGACTAGC.TCATATAT GTACCAGC.ATGTATCA CCATTGCG.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   185               168               227
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CACAGTCT.TCATATAT CGTCTGAA.ATGTATCA CCACAATG.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   277                87               189
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CAAGTGAC.TCATATAT AAGTACCT.ATGTATCA CCTTATGT.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                    81               210               291
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CAGAAGAA.ATGTATCA CTTGTTGG.TCATATAT AACCAATC.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   114               222                88
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            ATTCTCCA.ATGTATCA ACTTCAAC.ATGTATCA CACATGGT.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                    84               136               306
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CAAGTAGT.ATGTATCA CTTCTGGC.ATGTATCA GGTGTGAC.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   282                62               164
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            TGAACTCT.TCATATAT TGGTGGAA.TCATATAT ATTCGCAG.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   220               172               240
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            TGTAAGAC.ATGTATCA GTGTCCAT.ATGTATCA CTAAGGCG.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   151               193               182
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CAACTCCG.ATGTATCA ACCTGAGC.ATGTATCA ACCGACCA.ATGTATCA
## DDX11L1                    0                 0                 0
## WASH7P                   177               138               120
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            CAACCGTG.ATGTATCA TCAGATAC.ATGTATCA TGGTGACT.TCATATAT
## DDX11L1                    0                 0                 0
## WASH7P                   197               242               114
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
##            ATAGATCC.TCATATAT CCAGGTAA.TCATATAT CTGGTCGT.ATGTATCA
## DDX11L1                    0                 0                14
## WASH7P                   113               117               274
## MIR1302-11                 0                 0                 0
## FAM138A                    0                 0                 0
## OR4G4P                     0                 0                 0
## 95561 more rows ...
## 
## $samples
##                     group lib.size norm.factors treatment dose
## TTCCATTC.ATGTATCA KCR8580 27215440            1      PFNA   10
## TACAGAGT.ATGTATCA KCR7953 30307669            1       DDE  0.1
## TCAAGGAT.TCATATAT KCR8195 57944377            1      DMSO    0
## CCACAATG.TCATATAT KCR7889 36884641            1       BPS  0.1
## CTGGTCGT.TCATATAT KCR7889 46858022            1       BPS   10
## 118 more rows ...
## 
## $genes
##       SYMBOL         ENSEMBL  ENTREZID
## 1    DDX11L1 ENSG00000223972 100287102
## 2     WASH7P            <NA>    653635
## 3 MIR1302-11 ENSG00000283801 100422919
## 4    FAM138A ENSG00000237613    645520
## 5     OR4G4P ENSG00000268020     79504
##                                                      GENENAME Length
## 1                  DEAD/H-box helicase 11 like 1 (pseudogene)   1756
## 2                           WASP family homolog 7, pseudogene   2073
## 3                                            microRNA 1302-11   1021
## 4                family with sequence similarity 138 member A   1219
## 5 olfactory receptor family 4 subfamily G member 4 pseudogene    947
## 95561 more rows ...

3 Data pre-processing & QC

3.1 Filter lowly expressed genes

The counts dataset will contain genes that are expressed under certain experimental conditions and samples, but not in others. However, there are some genes that are unexpressed throughout all samples or contain very low gene counts not due to experimental conditions (i.e. background noise). These samples with low or zero read counts across all sample libraries should not be included within downstream differential expression analysis.

As discussed by Law et al. (2018b) and Phipson et al. (2020), there are multiple reasons for filtering out these lowly expressed genes prior to downstream analyses:

• From a statistical standpoint, there is interference with approximations such as false discovery rates, mean-variance relationship, reducing power, and multiple testing burdens needed when trying to detect differentially expressed genes (Chen, Lun, and Smyth 2016; Phipson et al. 2020).

• From a biological standpoint, genes that are not expressed at any level in response to a condition across all samples are likely not interesting to begin with (Law et al. 2018b).

In our Komen re-run samples, we see that approximately ~35% of genes have zero counts across all 123 samples. This is also shown in Figure 1A.

#Summary of rows w/ TRUE across all sample columns 
table(rowSums(split.DGElist[["komenredo.counts"]]$counts == 0) 
      == ncol(split.DGElist[["komenredo.counts"]]$counts))

## 
## FALSE  TRUE 
## 62485 33081

#Optional: Save a copy of the DGEList prior to filtering for plot comparisons
pre.filtered.raw <- split.DGElist[["komenredo.counts"]]

To automatically filter out these lowly expressed genes and keep as many worthwhile gene counts as possible, we can use the filterByExpr in the edgeR package (Robinson, McCarthy, and Smyth 2010). To quote the documentation:

“The filtering keeps genes that have count-per-million (CPM) above k in n samples, where k is determined by min.count and by the sample library sizes and n is determined by the design matrix. […] In addition, each kept gene is required to have at least min.total.count reads across all the samples.”

Chen, Lun, and Smyth (2016)

For the n smallest group sample size, filterByExpr will take either the design matrix or group as an argument (Chen, Lun, and Smyth 2016). The default function will keep genes with approximately ~10 read counts or more in the n minimum sample size. Specifically, the filtering uses CPM values to avoid differential bias by library size; namely, larger library sizes have lower CPM cutoffs because of improved confidence in the resolution of low gene expression levels, whereas smaller library sizes have poorer sensitivity to explore low-expression levels, and therefore require higher CPM cutoffs (Law et al. 2018b). This allows for robust and flexible cutoffs based on the experimental design and sequencing depths.

For our purpose, we will use the chemical treatment as our baseline design factor to determine worthwhile sample groups. As we performed in the DGEList conversion step, this information is stored in the split.DGElist$komenredo.counts$samples$treatment tab of our DGEList. ⊕Tip: You can confirm this yourself by typing in ‘median(split.DGElist[[komenredo.counts]] $samples $lib.size)’. To further explore ‘under the hood’ of the filterByExpr function, we see that our median library size in the Komen re-run experiment is 31579865 or approx. ~32 million.

⊕NOTE: Technically, the cpm(x, log = T) transformation returns ‘pseudo-counts’, which are calculated as log2(CPM + 2/L), where 2 is the prior count and L is the average library size in millions. This offset helps to avoid errors with logarithm of 0 values while ensuring identical counts have identical log-CPM values. For more details, check out the side note section and the guide by Law et al (2018). This means that the filterByExpr keeps genes that have a CPM of 10/31579865 = approx. ~0.32 CPM or more in at least n samples in a chemical treatment. For example, in the ‘PFNA’ treatment, a biologically interesting gene should be expressed in at least n = 9 samples because every patient-derived cell line has 9 total samples for a given chemical treatment, not including the water/DMSO controls (i.e. 3 doses * 3 technical replicates for each biological replicate).

# Use filterByExpr to automatically filter counts 
split.DGElist[["komenredo.counts"]] <-
  #Subset the genes (i.e. rows) using chemical treatment
  #as the min.group size filter
  split.DGElist[["komenredo.counts"]][
  filterByExpr(split.DGElist[["komenredo.counts"]], 
               group = split.DGElist$komenredo.counts$samples$treatment), ,
  keep.lib.sizes = FALSE]

⊕NOTE: The counts were directly subsetted and stored back as the new DGEList instead of creating an intermediary variable.

#Check out how many genes were filtered
dim(split.DGElist[["komenredo.counts"]])

## [1] 42363   123

 

Using this filtering criteria, we see the number of genes is reduced from 95566 to 42363 genes across all 123 samples, about a ~56% decrease in the number of genes that we started with (Figure 1B). Additionally, by subsetting the entire DGEList-object, this also removed both the counts and the associated gene information for the filtered rows, while correctly retaining the worthwhile counts and its associated information.

For a comparison between un-filtered and filtered gene count distributions, see Figure 1 for density plots of the log2-CPM values in the Komen re-run experiment. The code used to produce these density plots is also provided below.⁴

Show/Hide Code

#Optional: When creating and publishing plots to PDFs, use par to specify the grid 
# and mfrow to specify how many plots on each page (vector for rows x columns)
par(mfrow=c(1,2))

#Density plots for each Sample separated by Treatment x Dose 

# A. Pre-filtered raw counts 
# First, reshape log2-cpm data into long format for ggplots2 plotting aesthetics
#   Note: melt() from reshape2 package converts matrix from wide-to-long
 cpm(pre.filtered.raw, log = TRUE) %>%

#  Matrix with two columns of text and one with the integer counts 
  melt(., value.name = "Count", varnames = (c('Symbol', 'sample.id'))) %>% 

#  Combine with corresponding metadata for facet splits
#   join data.frames with split.metadata.list[["komenredo.metadata"]]
#   Note: Only the relevant metadata columns are subsetted to save memory 
  left_join(., split.metadata.list[["komenredo.metadata"]][, 7:10], by = c('sample.id')) %>% 

# Overview of ggplots2 plotting functions
#  Note: Make sure to use data.frame objects from the DGEList
  
#  Introduce plotting aesthetics
  ggplot(., aes(x = Count, fill = Sample, col = Sample)) +
#  Choose type of plot geometry and opacity
    geom_density(alpha = 0.15) +
  
#  Add vertical line to visualize filtering cutoff threshold 
#  and change line type, color and size
    geom_vline(
      xintercept = 
        log2(10/(median(pre.filtered.raw$samples$lib.size)*1e-6)
             + 2/(mean(pre.filtered.raw$samples$lib.size)*1e-6)),
      linetype="dashed", size=0.7) +

#  Edit axes and legend titles
    labs(x = "log2-CPM", y = "Density") +
    ggtitle("A. Raw Data: Pre-filtered Counts") +
#  Edit background theme and/or other elements (i.e. element_text(), element_line)
    theme_bw() +
    theme(legend.justification = "bottom") +
    theme(plot.title = element_text(color="black", size=14, face="bold.italic")) +
#  Facets to subset sub-sections or separate multiple plots
#   Note 1: _R_ syntax "~" means "is dependent on"
#   Note 2: Axis scaling is set to be the same by default
#           Scaling for grid can be set free using "free" for both axes
#           and reformulate
    facet_wrap(reformulate("Dose", "Treatment"), scales = "free", nrow = 3)


#B. Post-filtered raw data (same process as above)
 cpm(split.DGElist[["komenredo.counts"]], log = TRUE) %>%
  melt(., value.name = "Count", varnames = (c('Symbol', 'sample.id'))) %>% 
  left_join(., split.metadata.list[["komenredo.metadata"]][, 7:10], by = c('sample.id')) %>% 

# Overview of ggplots2 plotting functions
#  Note: Make sure to use data.frame objects from the DGEList
  ggplot(., aes(x = Count, fill = Sample, col = Sample)) +
    geom_density(alpha = 0.15) +
    #Note: The log2-CPM cutoff threshold is prior to filtering
    geom_vline(xintercept = 
        log2(10/(median(pre.filtered.raw$samples$lib.size)*1e-6)
             + 2/(mean(pre.filtered.raw$samples$lib.size)*1e-6)),
      linetype="dashed", size=0.7) +
    labs(x = "log2-CPM", y = "Density") +
    ggtitle("B. Filtered Data: Post-filtered Counts") +
    theme_bw() +
    theme(legend.justification = "bottom") +
    theme(plot.title = element_text(color="black", size=14, face="bold.italic")) +
    facet_wrap(reformulate("Dose", "Treatment"), scales = "free", nrow = 3)

Figure 1: Density plots of overall gene expression for A.) pre-filtered and B.) post-filtered raw counts data within each chemical treatment x dose (uM) split by sample
The x-axes are log2-CPM (counts per million) scaled for all plots. A.) Overall expression distributions for sample cell-line groups are heavily right-skewed prior to filtering. Most genes are lowly-expressed or non-expressed with small or negative log2-CPM values.B.) Filtering out irrelevant genes preserves the right-skewed trend and retains only genes with worthwhile counts. Dotted vertical lines mark the log2-CPM threshold (equivalent to a CPM value of approx. ~0.38) used in the filtering step.

Here is an animated version of Figure 1 that helps visualize the magnitude of difference from the filtering step:

Show/Hide Code

#Optional: Store the ggplot object frames to pass into gganimate
# Warning: This takes awhile to render 

library(gganimate)
library(transformr)

# A. Pre-filtered raw counts 
pre.filterdensity.ggplot <- cpm(pre.filtered.raw, log = TRUE) %>%
  melt(., value.name = "Count", varnames = (c('Symbol', 'sample.id'))) %>% 
  left_join(., split.metadata.list[["komenredo.metadata"]][, 7:10], by = c('sample.id')) %>% 
  #Important: Create a constant value column for the graph title cycle 
  mutate(transition = "A. Raw Data: Pre-filtered Counts")

#B. Post-filtered raw data
post.filterdensity.ggplot <- cpm(split.DGElist[["komenredo.counts"]], log = TRUE) %>%
  melt(., value.name = "Count", varnames = (c('Symbol', 'sample.id'))) %>% 
  left_join(., split.metadata.list[["komenredo.metadata"]][, 7:10], by = c('sample.id')) %>% 
  #Important: Create a constant value column for the graph title cycle
  mutate(transition = "B. Filtered Data: Post-filtered Counts")

#Merge dataframes 
all.filterdensity.ggplot <- rbind(pre.filterdensity.ggplot, post.filterdensity.ggplot)

all.filterdensity.gganim <- all.filterdensity.ggplot %>% 
  ggplot(., aes(x = Count, fill = Sample, col = Sample)) +
    geom_density(alpha = 0.15) +
    #Note: The log2-CPM cutoff threshold is prior to filtering
    geom_vline(xintercept = 
        log2(10/(median(pre.filtered.raw$samples$lib.size)*1e-6)
             + 2/(mean(pre.filtered.raw$samples$lib.size)*1e-6)),
      linetype="dashed", size=0.7) +
    theme_bw() +
    theme(legend.justification = "bottom") +
    theme(plot.title = element_text(color="black", size=14, face="bold.italic")) +
    facet_wrap(reformulate("Dose", "Treatment"), scales = "free", nrow = 3) + 
    #Use the constant value column we created as the cycle titles
    labs(title = "{closest_state}", x = "log2-CPM", y = "Density") +
#Animation arguments
#  Define variable/values on how data should be transformed  
    transition_states(
        transition,
        transition_length = 1.5, #length of transition animation
        state_length = 1 #how long to say on a certain state
      ) +
#  Additional animation aesthetics
      enter_fade() + 
      exit_shrink() +
      ease_aes('sine-in-out') + 
    view_follow()

# Animate ggplot 
animate(all.filterdensity.gganim, fps = 15, height = 12, 
  width = 15, units = "in", res = 150)
#optional: Save the file to your wd()
anim_save("filtering_comparison.gif")

 

Side Note: Why do we use raw-scale transformations?

Although we may operate and visualize raw counts, differential gene expression and downstream analyses are almost never evaluated at the raw counts level (Law et al. 2018b). This is because there are various potential biases that can influence and misrepresent our results. For instance, the relative number of transcript reads mapped to a gene is affected by sequencing depth (i.e. concentrations loaded onto flow cells, quality scores/QC checks, chemistry artefacts), the length of a gene (i.e. longer genes map more transcripts), gene isoforms/alternative splicing, and other library preparation factors (i.e. RNA enrichment selection, software/instrumentation, reagents, sample preparations, protocols, etc.) (Evans, Hardin, and Stoebel 2017; Johnson and Krishnan 2022). These various technical effects impact the effective library size and composition and obfuscate actual biological effects due to experimental conditions. As such, we adjust the relative expression levels to achieve more valid comparisons either within or between samples.

⊕NOTE: As previously referenced, the log2-CPM cutoff threshold for the ‘pseudo-counts’ is actually calculated as log2(10/M + 2/L), where M is the median library size, 2 is the prior count, and L is the average library size in millions. In our example, the minimum log-CPM is log2(2/(31852429 * 1e-6)) = ~ -3.99, or in other words, after adding the prior count offset (2/L), a log2-CPM value of -3.99 maps to a gene count of 0 for the dataset. For more details, check out the guide by Law et al (2018). In our filterByExpr example above, we used log2 counts-per-million (CPM) because it scales the counts by the number of transcript fragments sequenced and accounts for differences in sequencing depth between sample libraries; namely, each gene count is expressed as a proportion of the total number reads within a sample (Johnson and Krishnan 2022). In addition, the counts data is not normally distributed as seen with the multi-modal peaks and long right-tail in Figure 1B. However, log2-CPM does not adjust for gene length. For our Komen re-run comparisons, we assume gene lengths remain constant and that there are no major differences in isoform usage between experimental conditions (Law et al. 2018b). To ensure that observed biological effects are due to experimental conditions rather than gene lengths, additional QC checks were also performed upstream during featureCounts alignment and mapping using splice-aware alignment tools.

3.2 Normalize gene expression distributions

Often, there is ‘undesirable’ batch variation from experimental conditions as previously discussed for the reasons above. Therefore, technical effects unrelated to the biological factors of interest need to be accounted for when examining expression differences between samples. Ideally, all samples in an experiment would have a similar range and distribution of expression values for between-sample comparisons (Law et al. 2018b). Following our filtering step, let’s examine the sample expression distributions to detect any abnormalities.

To extend on the information from the density plots in Figure 1B, we are also interested in looking at summary statistics such as the center, spread, and any outliers of the numerical data. A nifty visualization we can use is the box-violin plot — a combination of a box plot and violin plot overlayed on top of each other. From panel A of Figure 2, we see the spread and median of the un-normalized log2-CPM expression values varies widely across different samples. Specifically, the notches of the box-violin plots approximate the 95% confidence intervals for the sample median:

\[\begin{equation} median\pm 1.57\times\frac{IQR}{\sqrt{n}} \tag{1} \end{equation}\]

Although our raw counts data observes a non-gaussian, right-skewed distribution, we generally see that many of the confidence intervals for the log2-CPM medians do not overlap (Figure 2A). That is, we are 95% confident that the medians do significantly differ.

To address these discrepancies in expression distributions, a common approach is to use the calcNormFactors trimmed mean of M-values (TMM) method for between-sample normalizations (Robinson and Oshlack 2010). To briefly overview the method documentation:

“TMM normalizes across samples by finding a subset of genes whose variation is mostly due to technical rather than biological factors, i.e., not differentially expressed, then using this subset to calculate a scaling factor to adjust each sample. In brief, each sample is compared to a chosen reference sample. A certain upper and lower percentage of data based on absolute intensity and log-fold-change relative to the reference sample is removed (by default, 5% for absolute intensity and 30% for log-fold-change) and the log-fold-changes of the remaining set of genes are used to calculate a single scaling factor for the non-reference samples.”

Johnson and Krishnan (2022); Robinson and Oshlack (2010)

In short, TMM is a robust method that identifies a reference sample and filters out biased genes per each sample to calculate scaling factors for library size and composition normalization (Robinson and Oshlack 2010).⁵ When using the calcNormFactors function to calculate scaling factors, the raw counts data are not directly modified nor stored. Instead, the normalization factors for effective library sizes are automatically stored in the DGEList-object path, ~$samples$norm.factors, and are applied automatically in functions and downstream analyses (Law et al. 2018b).

For our Komen re-run dataset, the effects of TMM-normalization are noticeable as the magnitude of scaling factors range from ~ 0.61 to 1.76. These normalization factors are used to multiply across sample libraries. Specifically, a factor below one indicates downscaling of the library size relative to other sample libraries (Phipson et al. 2020). This suggests a limited pool of genes with high counts dominated the sequencing depth, which lead to lower than usual counts assigned for other genes in the library (Chen, Lun, and Smyth 2016). As such, these scaling factors below one would also upscale individual gene counts in a sample. Likewise, scaling factors above one upscale the total library size relative to other samples, but downscale certain individual gene counts (Phipson et al. 2020). Scaling factors close to the default value of 1 indicate limited need for correction factors with TMM normalization. Together, TMM normalization suppresses composition bias while preserving gene expression trends across all samples (Phipson et al. 2020). To further visualize the effects of post-TMM normalization, see Figure 2B.

#Optional: Save a copy of the DGEList prior to normalization for plot comparisons
pre.norm.raw <- cpm(split.DGElist[["komenredo.counts"]], log = TRUE) %>%
  melt(., value.name = "Count", varnames = (c('Symbol', 'sample.id'))) %>% 
  left_join(., split.metadata.list[["komenredo.metadata"]][, 7:10], by = c('sample.id'))

#Apply normalization to DGEList 
# Note: You can specify a different normalization method if desired; default is TMM 
# (i.e. upper quartile, relative log expression, etc.) 
split.DGElist[["komenredo.counts"]] <- calcNormFactors(split.DGElist[["komenredo.counts"]]
                                                       , method = "TMM")

#View the normalization scaling factors
split.DGElist[["komenredo.counts"]]$samples$norm.factors

##   [1] 1.3163756 0.6727679 0.8456147 1.1030240 1.0932634 1.3152815 1.2683598
##   [8] 1.0995873 1.0621392 1.1540998 0.7612806 0.6676836 0.6713808 1.0920510
##  [15] 0.6709672 1.3844889 1.3231433 0.7438119 1.3181909 1.3776268 1.1232266
##  [22] 1.0840759 1.3142513 1.1061944 1.0637321 1.0565824 1.3013334 1.3170761
##  [29] 0.7519843 0.7472611 1.4952428 1.3141601 1.3227213 1.1417239 1.1701010
##  [36] 1.1640061 1.2198653 0.6815565 1.2811878 1.2103913 1.0845492 0.7445676
##  [43] 1.1053757 1.3590930 0.7234861 0.7018611 1.1393005 1.2504355 1.0599162
##  [50] 0.6941835 0.7087857 1.3082926 1.3193446 1.4090428 1.2884216 1.3052159
##  [57] 1.2116470 1.0697078 0.7865119 0.6903150 1.0646595 1.0848674 0.7285894
##  [64] 0.6954696 1.3363950 1.2930512 1.1082730 1.0873699 1.4273149 0.7256032
##  [71] 1.2875959 0.7203007 0.7312686 1.1241101 1.3406057 0.6865820 1.2892630
##  [78] 1.5843953 0.6107289 0.7168018 1.1124341 0.7293839 1.1069805 1.4391735
##  [85] 1.1591030 0.7912437 0.6825186 0.6948463 0.6785224 0.6766418 1.0792634
##  [92] 0.7248792 0.7441181 1.0512682 0.7685388 0.7276274 1.7536990 0.6956993
##  [99] 0.6811815 0.7616933 1.0906275 0.7267584 1.3711341 0.7294075 0.7157972
## [106] 1.2472495 1.3766919 0.7194871 1.0694490 1.4513308 0.7304995 0.7323523
## [113] 1.2950627 1.1763331 1.3471523 0.7014517 1.4348133 1.3026813 0.6803589
## [120] 1.2962515 1.1896049 1.1504587 0.7226049

Show/Hide Code

#Notched box-violin plots for each Treatment x Dose split by Sample

# A. Pre-normalization 
#  Introduce plotting aesthetics
#   i.e. log2-CPM (y-axis) grouped by treatment x dose (x-axis; needs to be factor)
#        which is further split by sample group
  ggplot(pre.norm.raw, aes(x = interaction(Treatment, Dose), y = Count, fill = Sample)) +

#  Choose plot geometries and opacities/display settings
#  Violin Plot
    geom_violin(alpha=0.75, position = position_dodge(width = .75), size=1, color=NA) +

#  Notched boxplot  
  stat_boxplot(geom = "errorbar") +
  geom_boxplot(notch = TRUE, color="black",lwd=1, alpha = 0.5) +
  
#  Add a red horizontal line to visualize median log2CPM across all samples 
    geom_hline(yintercept = median(pre.norm.raw$Count), linetype="dashed", color = "red") +

#  Edit axes and legend titles
    labs(x = "Treatment x Dose (uM)", y = "Log2 counts per million") +
    ggtitle("A. Notched box-violin plots of log2CPMs (un-normalized)") +
    
#  Edit background theme and/or other elements
    theme(legend.justification = "bottom") +
    theme(plot.title = element_text(color="black", size=14, face="bold.italic")) + 
    theme_bw() +

#   Optional: Use viridis or rcolorbrewer for color schemes
    scale_fill_viridis_d(option = "viridis")


# B. Post-normalization 
 post.norm.raw <- cpm(split.DGElist[["komenredo.counts"]], log = TRUE) %>%
 melt(., value.name = "Count", varnames = (c('Symbol', 'sample.id'))) %>% 
  left_join(., split.metadata.list[["komenredo.metadata"]][, 7:10], by = c('sample.id'))
#  Introduce plotting aesthetics
#   i.e. log2-CPM (y-axis) grouped by treatment x dose (x-axis; needs to be factor)
#        which is further split by sample group
  ggplot(post.norm.raw, aes(x = interaction(Treatment, Dose), y = Count, fill = Sample)) +

#  Choose plot geometries and opacities/display settings
#  Violin Plot
    geom_violin(alpha=0.75, position = position_dodge(width = .75), size=1, color=NA) +

#  Notched boxplot  
  stat_boxplot(geom = "errorbar") +
  geom_boxplot(notch = TRUE, color="black",lwd=1, alpha = 0.5) +
  
#  Add a red horizontal line to visualize median log2CPM across all samples 
    geom_hline(yintercept = median(post.norm.raw$Count), linetype="dashed", color = "red") +

#  Edit axes and legend titles
    labs(x = "Treatment x Dose (uM)", y = "Log2 counts per million") +
    ggtitle("B. Notched box-violin plots of log2CPMs (TMM normalized)") +
    
#  Edit background theme and/or other elements
    theme(legend.justification = "bottom") +
    theme(plot.title = element_text(color="black", size=14, face="bold.italic")) + 
    theme_bw() +

#   Optional: Use viridis or rcolorbrewer for color schemes
    scale_fill_viridis_d(option = "viridis")

Figure 2: Notched box-violin plots of gene expression for A.) pre-normalized and B.) post-normalized log2-CPM (counts per million) data for each chemical treatment x dose (uM) split by sample
The log2 counts-per-million (log2-CPM) values are on the y-axis. A.) The spread and median of the un-normalized log2-CPM expression values vary widely across different samples. Confidence intervals for the log2-CPM median show discordance at α = 0.05. B.) Normalization with TMM preserves the right-skewed, non-gaussian trend and helps standardize the expression distribution. Notches approximate the 95% confidence intervals for the sample median. Dotted horizontal line corresponds to the median log2-CPM across all samples.

Here is an animated version of Figure 2 to visualize the performance of TMM normalization:

Show/Hide Code

#Optional: Store the ggplot object frames to pass into gganimate
# Warning: This takes awhile to render 

# A. Pre-normalization 
pre.norm.ggplot <- pre.norm.raw %>% 
  #Important: Create a constant value column for the graph title cycle 
  mutate(transition = "A. Notched box-violin plots of log2CPMs (un-normalized)")

# B. Post-normalization 
post.norm.ggplot <- post.norm.raw %>% 
  #Important: Create a constant value column for the graph title cycle
  mutate(transition = "B. Notched box-violin plots of log2CPMs (TMM normalized)")

#Merge dataframes 
all.norm.ggplot <- rbind(pre.norm.ggplot, post.norm.ggplot)

all.norm.gganim <- all.norm.ggplot %>% 
  ggplot(., aes(x = interaction(Treatment, Dose), y = Count, fill = Sample)) +
  geom_violin(alpha=0.75, position = position_dodge(width = .75), size=1, color=NA) +
  stat_boxplot(geom = "errorbar") +
  geom_boxplot(notch = TRUE, color="black",lwd=1, alpha = 0.5) +
  geom_hline(yintercept = median(all.norm.ggplot$Count), linetype="dashed", color = "red") +
    theme(legend.justification = "bottom") +
    theme(plot.title = element_text(color="black", size=14, face="bold.italic")) + 
    theme_bw() +
    scale_fill_viridis_d(option = "viridis") +
    #Use the constant value column we created as the cycle titles
  labs(title = "{closest_state}", x = "Treatment x Dose (uM)", y = "Log2 counts per million") +

#Animation arguments
#  Define variable/values on how data should be transformed  
    transition_states(
        transition,
        transition_length = 1.5, #length of transition animation
        state_length = 1 #how long to say on a certain state
      ) +
#  Additional animation aesthetics
      enter_fade() + 
      exit_shrink() +
      ease_aes('sine-in-out') 

# Animate ggplot 
animate(all.norm.gganim, fps = 15, height = 15, 
  width = 15, units = "in", res = 150)
#optional: Save the file to your wd()
anim_save("TMM_norm_comparison.gif")

3.3 Unsupervised clustering with multidimensional scaling plot (MDS)

As highlighted by Law et al. (2018b) and Phipson et al. (2020), an important plot for quality control and exploratory analysis of RNA-seq expression data is the multidimensional scaling plot (MDS). We need to perform quality checks on our data and confirm whether to re-evaluate/exclude samples from downstream analysis. In other words, we need to confirm the main source of variation in the expression signatures of our samples was due to experimental conditions and not ‘unwanted’ confounding.

In simple scenarios with two features or less (i.e. genes), we could utilize scatter plots or other basic visualizations to compare the expression levels between samples and confirm clusters of similarities/differences (McDermaid et al. 2018). However, even after our filtering step, our normalized counts matrix contains an immense amount of transcription data (i.e. 42363 genes x 123 samples). It is impossible to manually perform all pairwise combinations of expression levels and visualize these vast dimensions. An efficient way to overcome this hurdle is to generate a Multidimensional Scaling (MDS) Plot, an unsupervised dimensionality reduction technique that allows us to visualize distances and clusters of separation between samples in a 2-D graph without having to specify groups (Law et al. 2018b; Phipson et al. 2020).

Using the MDS plot (Figure 3, left) and an accompanying scree plot (Figure 3, right), we can condense the gene expression information across all samples and confirm whether we expect to find interesting differences prior to any downstream analyses. We use the function glimmaMDS from the glimma package to create the plot. Here are some benefits to using the interactive glimma plot rather than a static display (Su et al. 2017):

• Hovering over individual MDS data point projections will reveal additional information about the sample (Figure 3, left)
• Customizable labeling aesthetics such as scaling, coloration, and shapes to enhance cluster identification with multiple experimental designs and factors of interest
• Select which Principal Component dimensions are plotted in the MDS plot
• Examine the proportion of variation (i.e. eigenvalues) explained by multiple Principal Component dimensions in the scree plot (Figure 3, right)
• Append annotations that need edits or were not included upstream

To gauge whether our experimental design factors contribute meaningful expression differences, we will examine how our Komen re-run samples cluster and separate in the dimensions listed. For the MDS demonstration, the Euclidean distances for the Principle Coordinate Analysis are calculated using the average (i.e. root-mean-square) log2-fold changes for the top 500 genes divergent between pairs of samples (Su et al. 2017; Law et al. 2018b).

Figure 3: Multidimensional scaling plot (MDS) (left) and scree barplot (right) of log2-CPM values over default dimensions 1 and 2
Principle Coordinate Analysis was performed using the Euclidean distance metric for the average (i.e. root-mean-square) log2-fold changes of the top 500 genes divergent between pairs of samples.

In the scree barplot (Figure 3, right), the first two dimensions represent the largest proportion of variation in log2-fold changes amongst the samples. When we take a closer look at the MDS plot (Figure 3, left), we see that dimension 1, the bulk source of variation, is explained by the experimental groups. That is, the samples primarily separate or cluster together in transcriptional patterns based on interindividual heterogeneity. Taking a closer look, although all samples cluster by group, the largest difference between ex-vivo cell lines are observed between patient-donors KCR7953 and KCR7518 over dimension 1 at approximately ~ 6 units (i.e. 2^6 = 64-fold leading fold change) (Chen, Lun, and Smyth 2016). If we were to compare between cell populations in these individuals, we might expect stark differences in the total number of differentially expressed genes (DEGs). Another way to interpret this is that the differential expression appears to be greater than the variance (i.e. inter-sample differences are larger than intra-sample differences), and therefore differential expression is likely to be detected (Phipson et al. 2020). In contrast, comparing samples KCR8519 and KCR7518 may exhibit a smaller difference in DEGs when performing pairwise comparisons. Additionally, there does not appear to be a clear separation by race, but rather by individual.

Following, we see that subsequent orthogonal combinations of dimensions have a much more subdued effect, where clustering by chemical treatment and dose appear to explain the remaining slivers of expression differences in dimensions 2 and 3, respectively. ⊕NOTE: The higher the dimension, the smaller the proportion of varation expalined. For instance, there may be limited evidence of differential expression for lower doses of chemical treatments (i.e. see clustering of KCR 7953). We can also confirm that technical replicates for samples of the same group successfully cluster together in the MDS plot (i.e. within-sample similarities versus between-sample differences). If there were batch effects or outliers, the MDS plot could also inform us on how to adjust the design matrix (Phipson et al. 2020).

Overall, the MDS plot helped to confirm that our Komen re-run experiment was successful and controlled well for potential batch effects and sources of error (Phipson et al. 2020). Our greatest sources of variation in the expression data are primarily attributed to the experimental conditions we are interested in such as groups and treatments. We can therefore proceed with linear modelling of these experimental design factors in differential gene testing and downstream analyses. Horay! Stay tuned for Part 2: Differential Expression Analysis…

Side Note: More on MDS and how it works…

In our example above, we performed MDS using the Euclidean distance metric and singular value decomposition (SVD), which is akin to Principle Coordinate Analysis. To review, MDS/PCoA with SVD starts by plotting the coordinate expression data across all n genes (i.e. rows) for each m sample (i.e. columns), finds the center of the data using the averaged gene measurements in each row across all samples, and utilizes this center as the origin change of basis (Starmer 2018). Specifically, a line of best fit that goes through the origin is adjusted until the orthogonal combinations minimizes the linear distance between data points and maximizes the sum of squared distances (i.e. eigenvalue) from the projected points to the origin; this line is a Principle Component (PC) (Tzeng, Lu, and Li 2008; Starmer 2018). Additional PCs are added by finding perpendicular lines to the previous PC(s) that go through the origin; the maximum number of PCs generated is the smaller number of either n variables (i.e. genes) or m samples (i.e. columns) (Tzeng, Lu, and Li 2008; Starmer 2018). These principal components help explain how data are spread out along different linear combinations and informs the percent of variation accounted for by each axis (Starmer 2018).

Once all the linear combinations of PCs have been generated, the singular unit vectors (i.e. eigenvectors) are determined from the proportions of loading scores, or correlations between original variables (i.e. genes) and unit-scaled components (Tzeng, Lu, and Li 2008). Loading scores help determine which variables have the largest effect by projecting the sample coordinates onto the graph (Tzeng, Lu, and Li 2008). Variation around the origin is calculated by dividing the eigenvalue (i.e. sum of sq. distances for a PC) by the sample size - 1 (i.e. m - 1) (Starmer 2018). You can use the eigenvalues (i.e. sum of squared distances) to determine the proportion of variation accounted for by each PC. The scree plot shown on the right-hand side of Figure 3 is a graphical representation of the percentage of variation accounted for by each PC. Together, these transformations and projections help approximate the different patterns of variance and associations between variables in reduced dimensions. Alternatively, another commonly used approach is to perform eigen-decomposition on a covariance matrix, which is not discussed here (Tzeng, Lu, and Li 2008).

For more details, check out the references and footnotes.

Session info

For record-keeping and reproducibility purposes, this session information documents the versions of R and of the software/packages that were used in this pipeline.

## R version 4.2.0 (2022-04-22 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19044)
## 
## Matrix products: default
## 
## locale:
## [1] LC_COLLATE=English_United States.utf8 
## [2] LC_CTYPE=English_United States.utf8   
## [3] LC_MONETARY=English_United States.utf8
## [4] LC_NUMERIC=C                          
## [5] LC_TIME=English_United States.utf8    
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] Glimma_2.7.0         gplots_3.1.3         reshape2_1.4.4      
##  [4] forcats_0.5.1        stringr_1.4.0        dplyr_1.0.9         
##  [7] purrr_0.3.4          readr_2.1.2          tidyr_1.2.0         
## [10] tibble_3.1.7         tidyverse_1.3.2      Biostrings_2.65.1   
## [13] GenomeInfoDb_1.33.3  XVector_0.37.0       org.Mm.eg.db_3.15.0 
## [16] org.Hs.eg.db_3.15.0  AnnotationDbi_1.59.1 IRanges_2.31.0      
## [19] S4Vectors_0.35.1     Biobase_2.57.1       BiocGenerics_0.43.0 
## [22] edgeR_3.39.3         limma_3.53.4         viridis_0.6.2       
## [25] viridisLite_0.4.0    RColorBrewer_1.1-3   transformr_0.1.3    
## [28] gganimate_1.0.7      ggplot2_3.3.6        RefManageR_1.3.0    
## [31] bibtex_0.4.2.3       tufte_0.12.1         rmarkdown_2.14      
## [34] pander_0.6.5         gifski_1.6.6-1       bookdown_0.27       
## [37] BiocStyle_2.25.1    
## 
## loaded via a namespace (and not attached):
##   [1] readxl_1.4.0                backports_1.4.1            
##   [3] plyr_1.8.7                  splines_4.2.0              
##   [5] BiocParallel_1.31.10        digest_0.6.29              
##   [7] htmltools_0.5.3             fansi_1.0.3                
##   [9] magrittr_2.0.3              memoise_2.0.1              
##  [11] googlesheets4_1.0.0         tzdb_0.3.0                 
##  [13] annotate_1.75.0             modelr_0.1.8               
##  [15] matrixStats_0.62.0          lpSolve_5.6.15             
##  [17] prettyunits_1.1.1           colorspace_2.0-3           
##  [19] blob_1.2.3                  rvest_1.0.2                
##  [21] haven_2.5.0                 xfun_0.31                  
##  [23] crayon_1.5.1                RCurl_1.98-1.7             
##  [25] jsonlite_1.8.0              genefilter_1.79.0          
##  [27] survival_3.3-1              glue_1.6.2                 
##  [29] gtable_0.3.0                gargle_1.2.0               
##  [31] zlibbioc_1.43.0             DelayedArray_0.23.0        
##  [33] scales_1.2.0                DBI_1.1.3                  
##  [35] Rcpp_1.0.9                  xtable_1.8-4               
##  [37] progress_1.2.2              units_0.8-0                
##  [39] bit_4.0.4                   proxy_0.4-27               
##  [41] htmlwidgets_1.5.4           httr_1.4.3                 
##  [43] ellipsis_0.3.2              pkgconfig_2.0.3            
##  [45] XML_3.99-0.10               farver_2.1.1               
##  [47] sass_0.4.2                  dbplyr_2.2.1               
##  [49] locfit_1.5-9.6              utf8_1.2.2                 
##  [51] tidyselect_1.1.2            rlang_1.0.4                
##  [53] munsell_0.5.0               cellranger_1.1.0           
##  [55] tools_4.2.0                 cachem_1.0.6               
##  [57] cli_3.3.0                   generics_0.1.3             
##  [59] RSQLite_2.2.15              broom_1.0.0                
##  [61] evaluate_0.15               fastmap_1.1.0              
##  [63] yaml_2.3.5                  knitr_1.39                 
##  [65] bit64_4.0.5                 fs_1.5.2                   
##  [67] caTools_1.18.2              KEGGREST_1.37.3            
##  [69] xml2_1.3.3                  compiler_4.2.0             
##  [71] rstudioapi_0.13             png_0.1-7                  
##  [73] e1071_1.7-11                reprex_2.0.1               
##  [75] geneplotter_1.75.0          tweenr_1.0.2               
##  [77] bslib_0.4.0                 stringi_1.7.8              
##  [79] lattice_0.20-45             Matrix_1.4-1               
##  [81] classInt_0.4-7              vctrs_0.4.1                
##  [83] pillar_1.8.0                lifecycle_1.0.1            
##  [85] BiocManager_1.30.18         jquerylib_0.1.4            
##  [87] bitops_1.0-7                GenomicRanges_1.49.0       
##  [89] R6_2.5.1                    KernSmooth_2.23-20         
##  [91] gridExtra_2.3               codetools_0.2-18           
##  [93] gtools_3.9.3                assertthat_0.2.1           
##  [95] SummarizedExperiment_1.27.1 DESeq2_1.37.4              
##  [97] withr_2.5.0                 GenomeInfoDbData_1.2.8     
##  [99] parallel_4.2.0              hms_1.1.1                  
## [101] grid_4.2.0                  class_7.3-20               
## [103] MatrixGenerics_1.9.1        googledrive_2.0.0          
## [105] sf_1.0-8                    lubridate_1.8.0

References

Carlson, Marc. 2022a. “Org.Hs.eg.db: Genome Wide Annotation for Human.”

———. 2022b. “Org.Mm.eg.db: Genome Wide Annotation for Mouse.”

Chen, Yunshun, Aaron T. L. Lun, and Gordon K. Smyth. 2016. “From Reads to Genes to Pathways: Differential Expression Analysis of RNA-Seq Experiments Using Rsubread and the edgeR Quasi-Likelihood Pipeline.” F1000Research 5 (August): 1438. https://doi.org/10.12688/f1000research.8987.2.

Evans, Ciaran, Johanna Hardin, and Daniel M Stoebel. 2017. “Selecting Between-Sample RNA-Seq Normalization Methods from the Perspective of Their Assumptions.” Briefings in Bioinformatics 19 (5): 776–92. https://doi.org/10.1093/bib/bbx008.

Johnson, Kayla A., and Arjun Krishnan. 2022. “Robust Normalization and Transformation Techniques for Constructing Gene Coexpression Networks from RNA-Seq Data.” Genome Biology 23 (1): 1. https://doi.org/10.1186/s13059-021-02568-9.

Law, Charity W., Monther Alhamdoosh, Shian Su, Xueyi Dong, Luyi Tian, Gordon K. Smyth, and Matthew E. Ritchie. 2018a. “RNA-Seq Analysis Is Easy as 1-2-3 with Limma, Glimma and edgeR.” F1000Research 5 (December): 1408. https://doi.org/10.12688/f1000research.9005.3.

———. 2018b. “RNA-Seq Analysis Is Easy as 1-2-3 with Limma, Glimma and edgeR.” F1000Research 5 (December): 1408. https://doi.org/10.12688/f1000research.9005.3.

McDermaid, Adam, Brandon Monier, Jing Zhao, Bingqiang Liu, and Qin Ma. 2018. “Interpretation of Differential Gene Expression Results of RNA-Seq Data: Review and Integration.” Briefings in Bioinformatics 20 (6): 2044–54. https://doi.org/10.1093/bib/bby067.

Oleś, Andrzej. 2022. “BiocStyle: Standard Styles for Vignettes and Other Bioconductor Documents.” https://github.com/Bioconductor/BiocStyle.

Pagès, H., P. Aboyoun, R. Gentleman, and S. DebRoy. 2022. “Biostrings: Efficient Manipulation of Biological Strings.” https://bioconductor.org/packages/Biostrings.

Pagès, Hervé, Marc Carlson, Seth Falcon, and Nianhua Li. 2022. “AnnotationDbi: Manipulation of SQLite-Based Annotations in Bioconductor.” https://bioconductor.org/packages/AnnotationDbi.

Phipson, Belinda, Anna Trigos, Matt Ritchie, Shian Su, Maria Doyle, Harriet Dashnow, and Charity Law. 2020. “RNA-Seq Analysis in R.” https://combine-australia.github.io/RNAseq-R/06-rnaseq-day1.html.

Robinson, Mark D, Davis J McCarthy, and Gordon K Smyth. 2010. “edgeR: A Bioconductor Package for Differential Expression Analysis of Digital Gene Expression Data” 26: 139–40. https://doi.org/10.1093/bioinformatics/btp616.

Robinson, Mark D, and Alicia Oshlack. 2010. “A Scaling Normalization Method for Differential Expression Analysis of RNA-Seq Data.” Genome Biology 11 (3): R25. https://doi.org/10.1186/gb-2010-11-3-r25.

Starmer, Joshua. 2018. “StatQuest: Principal Component Analysis (PCA), Step-by-Step,” April. https://www.youtube.com/watch?v=FgakZw6K1QQ.

Su, Shian, Charity W Law, Casey Ah-Cann, Marie-Liesse Asselin-Labat, Marnie E Blewitt, and Matthew E Ritchie. 2017. “Glimma: Interactive Graphics for Gene Expression Analysis.” Edited by Bonnie Berger. Bioinformatics 33 (13): 2050–52. https://doi.org/10.1093/bioinformatics/btx094.

Tzeng, Jengnan, Henry Horng-Shing Lu, and Wen-Hsiung Li. 2008. “Multidimensional Scaling for Large Genomic Data Sets.” BMC Bioinformatics 9 (1). https://doi.org/10.1186/1471-2105-9-179.

Footnotes

---

1. ¹The Javascript dependencies needed to render the paged tables are not included in the rmarkdown html output. As described in this post, one potential solution is to initialize the JS dependencies. However, this does not work with the ‘hide/show output’ bootstrap buttons. Another solution is to use the pander package, which only prints the output as static tables.↩︎

2. ²Tip: For additional ways to convert between gene id formats, check out this excellent video tutorial from Khushbu Patel.↩︎

3. ³Ontology information retrieval is optional if you are performing gene set testing later on with goana/CAMERA/ROAST/etc. However, in order to display this information within interactive glimma plots, you need to include and embed this information early on. We do not include ontology retrieval here to limit resource usage and processing times.↩︎

4. ⁴Tip: For a guide on using ggplots2 functions from the tidyverse package with DGEList objects, check out this excellent guide from Steve Pederson at the University of Adelaide, Australia.↩︎

5. ⁵For an in-depth, step-by-step breakdown of the TMM method, check out this excellent tutorial from Joshua Starmer, PhD.↩︎